Permeability of small molecules through a lipid bilayer: A multiscale simulation study

Journal of Physical Chemistry B

Volumn 113, Issue 35, 2009, Pages 12019-12029

  Orsi, Mario ^a   Sanderson, Wendy E ^b   Essex, Jonathan W ^a  

^a UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

^b JANSSEN RESEARCH AND DEVELOPMENT   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMS; CAPILLARITY; FREE ENERGY; LIPID BILAYERS; MOLECULAR DYNAMICS; MOLECULES; PERMEATION; PHOSPHOLIPIDS;

ATOMIC LEVELS; BI-LAYER; DIFFUSION COEFFICIENTS; DIFFUSION MODEL; EXPERIMENTAL DATA; FREE-ENERGY DIFFERENCE; GRAIN MODELS; MOLECULAR DYNAMICS SIMULATIONS; MULTI-SCALE APPROACHES; MULTI-SCALE SIMULATION; MULTISCALES; ORDERS OF MAGNITUDE; ORGANIC MOLECULES; PERMEABILITY COEFFICIENTS; PERMEABILITY PROPERTIES; PERMEATING MOLECULE; PHOSPHOLIPID BILAYER; SMALL MOLECULES; TRANSMEMBRANES;

SIMULATORS;

EID: 69649103938     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp903248s     Document Type: Article

References (87)

1. Pohorille, A.; Wilson, M. A. Cell. Mol. Biol. Lett. 2001, 6, 369-374.
2. Xiang, T.-X.; Anderson, B. D. Adv. Drug Delivery Rev. 2006, 58, 1357-1378.
3. Overton, E. Vierteljahrsschr. Naturforsch. Ges. Zuerich 1896, 41, 383.
4. Finkelstein, A. J. Gen. Physiol. 1976, 68, 127-135.
5. Diamond, J. M.; Katz, Y. J. Membr. Biol. 1974, 17, 121-154.
6. Diamond, J. M.; Szabo, G.; Katz, Y. J. Membr. Biol. 1974, 17, 148-152.
7. Marrink, S.-J.; Berendsen, H. J. C. J. Phys. Chem. 1994, 98, 4155-4168.
8. MacCallum, J. L.; Tieleman, D. P. In Computational Modeling of Membrane Bilayers; Feller, S. E., Ed.; Elsevier, New York, 2008; Chapter 8, pp 227-256.
9. Orsi, M.; Essex, J. W. In Molecular Simulations and Biomembranes: From Biophysics to Function; Biggin, P. C., Sansom, M. S., Eds.; Royal Society of Chemistry: in press.
10. Muller, M.; Katsov, K.; Schick, M. Phys. Rep. 2006, 434, 113-176.
11. Brannigan, G.; Lin, L. C. L.; Brown, F. L. H. Eur. Biophys. J. 2006, 35, 104-124.
12. Orsi, M.; Sanderson, W.; Essex, J. W. In Molecular InteractionsBringing Chemistry to Life; Hicks, M. G., Kettner, C., Eds.; BeilsteinInstitut: Germany, 2007; pages 185-205. (Also available online at http:// www.beilstein-institut. de/bozen2006/proceedings/Orsi/Orsi.pdf.)
13. Xiang, T.-X.; Anderson, B. D. J. Membr. Biol. 1994, 140, 111-122.
14. Ayton, G. S.; Noid, W. G.; Voth, G. A. Curr. Opin. Struct. Biol. 2007, 17, 192-198.
15. Woods, C. J.; Mulholland, A. J. In Chemical Modelling: Applications and Theory; Hinchliffe, A., Ed.; Royal Society of Chemistry: Cambridge, U.K., 2008.
16. Sherwood, P.; Brooks, B. R.; Sansom, M. S. P. Curr. Opin. Struct. Biol. 2008, 18, 630-640.
17. Abrams, C. F. J. Chem. Phys. 2005, 123, 234101.
18. Neri, M.; Anselmi, C.; Cascella, M.; Maritan, A.; Carloni, P. Phys. Rev. Lett. 2005, 95, 218102.
19. Neri, M.; Anselmi, C.; Carnevale, V.; Vargiu, A. V.; Carloni, P. J. Phys.: Condens. Matter 2006, 18, S347-S355.
20. Shi, Q.; Izvekov, S.; Voth, G. A. J. Phys. Chem. B 2006, 110, 15045-15048.
21. Ensing, B.; Nielsen, S. O.; Moore, P. B.; Klein, M. L.; Parrinello, M. J. Chem. Theory Comput. 2007, 3, 1100-1105.
22. Praprotnik, M.; Delle Site, L.; Kremer, K. Phys. Rev. E 2006, 73, 066701.
23. Praprotnik, M.; Delle Site, L.; Kremer, K. J. Chem. Phys. 2007, 126, 134902.
24. Praprotnik, M.; Matysiak, S.; Delle Site, L.; Kremer, K.; Clementi, C. J. Phys.: Condens. Matter 2007, 19, 292201.
25. Orsi, M.; Haubertin, D. Y.; Sanderson, W. E.; Essex, J. W. J. Phys. Chem. B 2008, 112, 802-815.
26. Michel, J.; Orsi, M.; Essex, J. W. J. Phys. Chem. B 2008, 112, 657-660.
27. Gay, J. G.; Berne, B. J. J. Chem. Phys. 1981, 74, 3316-3319.
28. Liu, Y.; Ichiye, T. J. Phys. Chem. 1996, 100, 2723-2730.
29. Fennell, C. J.; Gezelter, J. D. J. Chem. Phys. 2004, 120, 9175-9184.
30. Chandra, A.; Ichiye, T. J. Chem. Phys. 1999, 111, 2701-2709.
31. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
32. Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. J. Phys. Chem. 1987, 91, 6269-6271.
33. Tan, M.-L.; Brooks, B. R.; Ichiye, T. Chem. Phys. Lett. 2006, 421, 166-170.
34. Bemporad, D.; Essex, J. W.; Luttmann, C. J. Phys. Chem. B 2004, 708, 4875-4884.
35. Schaftenaar, G.; Noordik, J. H. J. Comput-Aided Mol. Des. 2000, 14, 123-134.
36. AMBER 8 User's Manual; University of California: San Francisco, CA, 2004.
37. Wang, J. M.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. J. Comput. Chem. 2004, 25, 1157-1174.
38. Jakalian, A.; Bush, B. L.; Jack, D. B. J. Comput. Chem. 2000, 21, 132-146.
39. Xiang, T.-X.; Chen, X. L.; Anderson, B. D. Biophys. J. 1992, 63, 78-88.
40. Feenstra, K. A.; Hess, B.; Berendsen, H. J. C. J. Comput. Chem. 1999, 20, 786-798.
41. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids, 1st ed.; Oxford Science Publications: Oxford, U.K., 1987.
42. Cleaver, D. J.; Care, C. M.; Allen, M. P.; Neal, M. P. Phys. Rev. E 1996, 54, 559-567.
43. Golubkov, P. A.; Ren, P. J. Chem. Phys. 2006, 125, 064103.
44. Price, S. L.; Stone, A. J.; Alderton, M. Mol. Phys. 1984, 52, 987-1001.
45. Marrink, S.-J.; Berendsen, H. J. C. J. Phys. Chem. 1996, 700, 16729-16738.
46. Roux, B.; Karplus, M. Biophys. J. 1991, 59, 961-981.
47. Roux, B.; Karplus, M. J. Phys. Chem. 1991, 95, 4856-4868.
48. BRAHMS: A Biomembrane Reduced-Approach Molecular Simulator, http://www.persorial.soton.ac.uk/OTsi/brahms/ (accessed July 28, 2009).
49. Dullweber, A.; Leimkuhler, B.; McLachlan, R. J. Chem Phys. 1997, 707, 5840-5851.
50. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Di Nola, A.; Haak, J. R. J. Chem. Phys. 1984, 87, 3684-3690.
51. The Iridis Compute Cluster, http://www.southampton.ac.uk/ isolutions/computing/hpc/iridis/ (accessed July 28, 2009).
52. Nagle, J. F.; Tristram-Nagle, S. Biochim. Biophys. Acta 2000, 1469, 159-195.
53. Xiang, T.-X.; Anderson, B. D. J. Membr. Biol. 1995, 148, 157-167.
54. Chiou, J.-S.; Krishna, P. R.; Kamaya, H.; Ueda, I. Biochim. Biophys. Acta 1992, 1110, 225-233.
55. Rottenberg, H. Biochemistry 1992, 31, 9473-9481.
56. Barry, J. A.; Gawrisch, K. Biochemistry 1994, 33, 8082-8088.
57. Holte, L. L.; Gawrisch, K. Biochemistry 1997, 36, 4669-4674.
58. Feller, S. E.; Brown, C. A.; Nizza, D. T.; Gawrisch, K. Biophys. J. 2002, 82, 1396-1404.
59. Patra, M.; Salonen, E.; Terama, E.; Vattulainen, I.; Faller, R.; Lee, B. W.; Holopainen, J.; Karttunen, M. Biophys. J. 2006, 90, 1121-1135.
60. MacCallum, J. L.; Bennett, W. F. D.; Tieleman, D. P. Biophys. J. 2008, 94, 3393-3404.
61. Johansson, A. C. V.; Lindahl, E. J. Chem Phys. 2009, 130, 185101.
62. Shinoda, W.; Mikami, M.; Baba, T.; Hato, M. J. Phys. Chem. B 2004, 108, 9346-9356.
63. Sugii, T.; Takagi, S.; Matsumoto, Y. J. Chem. Phys. 2005, 123, 184714.
64. Jedlovszky, P.; Mezei, M. J. Am. Chem. Soc. 2000, 122, 51255131.
65. Bassolino-Klimas, D.; Alper, H. E.; Stouch, T. R. Biochemistry 1993, 32, 12624-12637.
66. Bemporad, D.; Luttmann, C.; Essex, J. W. Biochim. Biophys. Acta 2005, 7778, 1-21.
67. Grossfield, A.; Woolf, T. B. Langmuir 2002, 18, 198-210.
68. Ulander, J.; Haymet, A. D. J. Biophys. J. 2003, 85, 3475-3484.
69. dos Santos, D. J. V. A.; Eriksson, L. A. Biophys. J. 2006, 91, 2464-2474.
70. Walter, A.; Gutknecht, J. J. Membr. Biol. 1986, 90, 207-217.
71. Alper, H. E.; Stouch, T. R. J. Phys. Chem. 1995, 99, 5724-5731.
72. Vaz, W. L. C.; Almeida, P. F. Biophys. J. 1991, 60, 1553-1554.
73. Orsi, M.; Sanderson, W. E.; Essex, J. W. submitted for publication.
74. Feller, S. E.; Mackerell, A. D. J. Phys. Chem. B 2000, 104, 7510-7515.
75. Sonne, J.; Jensen, M. Ø.; Hansen, F. Y.; Hemmingsen, L.; Peters, G. H. Biophys. J. 2007, 92, 4157-4167.
76. Paula, S.; Volkov, A. G.; Vanhoek, A. N.; Haines, T. H.; Deamer, D. W. Biophys. J. 1996, 70, 339-348.
77. Jansen, M.; Blume, A. Biophys. J. 1995, 68, 997-1008.
78. Lande, M. B.; Donovan, J. M.; Zeidel, M. L. J. Gen. Physiol. 1995, 706, 67-84.
79. Orbach, E.; Finkelstein, A. J. Gen. Physiol. 1980, 75, 427-436.
80. Hill, W. G.; Rivers, R. L.; Zeidel, M. L. J. Gen. Physiol. 1999, 114, 405-414.
81. Walter, A.; Gutknecht, J. J. Membr. Biol. 1984, 77, 255-264.
82. Bar-On, Z.; Degani, H. Biochim. Biophys. Acta 1985, 813, 207-212.
83. Nagle, J. F.; Mathai, J. C.; Zeidel, M. L.; Tristram-Nagle, S. J. Gen. Physiol. 2008, 131, 77-85.
84. Bloom, M.; Evans, E.; Mouritsen, O. G. Q. Rev. Biophys. 1991, 24, 293-397.
85. Carruthers, A.; Melchior, D. L. Biochemistry 1983, 22, 5797-5807.
86. Ceve, G.; Marsh, D. Phospholipid Bilayers-Physical Principles and Models, 1st ed.; John Wiley & Sons: New York, 1987.
87. Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graphics 1996, 14, 33-38.