Computer simulation of small moleculle permeation across a lipid bilayer: Dependence on bilayer properties and solute volume, size, and cross-sectional area

Biophysical Journal

Volumn 87, Issue 1, 2004, Pages 1-13

  Bemporad, D ^a   Luttmann, C ^b   Essex, J W ^a  

^a UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

^b SANOFI   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ACETAMIDE; ACETIC ACID; ACETIC ACID ESTER; BENZENE; DIPALMITOYLPHOSPHATIDYLCHOLINE; ETHANE; HEXADECANE; METHANOL; METHYL ACETATE; METHYLAMINE; NEW DRUG; OCTANOL; PHOSPHOLIPID; UNCLASSIFIED DRUG; WATER;

ARTICLE; CELL MEMBRANE TRANSPORT; COMPUTER SIMULATION; DIFFUSION COEFFICIENT; DRUG DESIGN; DRUG DIFFUSION; DRUG PENETRATION; DRUG SOLUBILITY; ENTROPY; LIPID MEMBRANE; MOLECULAR DYNAMICS; MOLECULAR SIZE; PARTITION COEFFICIENT; PHOSPHOLIPID BILAYER; SOLUTE;

EID: 3042813458     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.103.030601     Document Type: Article

References (78)

1. Alper, H. E., and T. R. Stouch. 1995. Orientation and diffusion of a drug analog in biomembranes-molecular dynamics simulations. J. Phys. Chem. 99:5724-5731.
2. Balaz, S. 2000. Lipophilicity in trans-bilayer transport and subcellular pharmacokinetics. Perspect. Drug Discov. Des. 19:157-177.
3. Bar-On, Z., and H. Degani. 1985. Permeability of alkylamines across phosphatidylcholine vesicles as studied by H-NMR. Biochim. Biophys. Acta. 813:207-217.
4. Bassolino-Klimas, D., H. E. Alper, and T. R. Stouch. 1993. Solute diffusion in lipid bilayer-membranes-an atomic-level study by molecular dynamics simulation. Biochemistry. 32:12624-12637.
5. Bassolino-Klimas, D., H. E. Alper, and T. R. Stouch. 1995. Mechanism of solute diffusion through lipid bilayer-membranes by molecular dynamics simulation. J. Am. Chem. Soc. 117:4118-4129.
6. Bean, R. C., W. C. Shepherd, and H. Chan. 1968. Permeability of lipid bilayer membranes to organic solutes. J. Gen. Physiol. 52:495-508.
7. Bemporad, D., J. W. Essex, and C. Luttmann. 2004. Permeation of small molecules through a lipid bilayer: a computer simulation study. J. Phys. Chem. B. 108:4875-4884.
8. Berendsen, H. J. C., and S. J. Marrink. 1993. Molecular dynamics of water transport through membranes: water from solvent to solute. Pure Appl. Chem. 65:2513-2520.
9. Bochain, A., L. Estey, G. Haronian, M. Reale, C. Rojas, and J. Cramer. 1981. Determination of catecholamine permeability coefficients for passive diffusion across phospholipid vesicle membranes. J. Membr. Biol. 60:73-76.
10. Bresseleers, G. J. M., H. L. Goderis, and P. P. Tobback. 1984. Measurement of the glucose permeation rate across phospholipid bilayers using small unilamellar vesicles. Biochim. Biophys. Acta. 772:374-382.
11. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM - a program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4:187-217.
12. Brown, M., J. Seelig, and U. Haberlein. 1979. Structural dynamics in phospholipid bilayers from deuterium spin-lattice relaxation time measurements. J. Chem. Phys. 70:5045-5053.
13. Brunner, J., D. E. Graham, H. Hauser, and G. Semenza. 1980. Ion and sugar permeabilities of lecithin bilayers: comparison of curved and planar bilayers. J. Membr. Biol. 57:133-141.
14. Cascales, J. J. L., J. G. H. Cifre, and J. G. de la Torre. 1998. Anaesthetic mechanism on a model biological membrane: a molecular dynamics simulation study. J. Phys. Chem. B. 102:625-631.
15. Cohen, B. E. 1975a. The permeability of liposomes to nonelectrolytes. I. Activation energies for permeation. J. Membr. Biol. 20:205-234.
16. Cohen, B. E. 1975b. The permeability of liposomes to nonelectrolytes. H. The effect of nystatin and gramicidin A. J. Membr. Biol. 20:235-268.
17. De Young, L. R., and K. A. Dill. 1988. Solute partitioning into lipid bilayer membranes. Biochemistry. 27:5281-5289.
18. Diamond, J. M., and Y. Katz. 1974. Interpretation of nonelectrolyte partition coefficients between dimyristoyl lecithin and water. J. Membr. Biol. 17:121-154.
19. Dix, J. A., D. Kivelson, and J. M. Diamond. 1978. Molecular motion of small nonelectrolyte molecules in lecithin bilayers. J. Membr. Biol. 40:315-342.
20. Feller, S. E., and R. W. Pastor. 1996. On simulating lipid bilayers with an applied surface tension: periodic boundary conditions and undulations. Biophys. J. 71:1350-1355.
21. Feller, S. E., and R. W. Pastor. 1999. Constant surface tension simulations of lipid bilayers: the sensitivity of surface areas and compressibilities. J. Chem. Phys. 111:1281-1287.
22. Feller, S. E., R. M. Venable, and R. W. Pastor. 1997. Computer simulation of a DPPC phospholipid bilayer: structural changes as a function of molecular surface area. Langmuir. 13:6555-6561.
23. Feller, S. E., Y. Zhang, R. W. Pastor, and B. R. Brooks. 1995. Constant pressure molecular dynamics simulation: the Langevin piston. J. Chem. Phys. 103:4613-4621.
24. Finkelstein, A. 1976. Water and nonelectrolyte permeability of lipid bilayer membranes. J. Gen. Physiol. 68:127-135.
25. Gutknecht, J., and A. Walter. 1981. Histamine, theophylline and tryptamine transport through lipid bilayer membranes. Biochim. Biophys. Acta. 649:149-154.
26. Hill, W. G., R. L. Rivers, and M. L. Zeidel. 1999. Role of leaflet asymmetry in the permeability of model biological membranes to protons, solutes, and gases. J. Gen. Physiol. 114:405-414.
27. Hockney, R. W. 1970. The potential calculation and some applications. Meth. Comp. Phys. 9:136-211.
28. Hoover, W. G. 1985. Canonical dynamics: equilibrium phase-space distributions. Phys. Rev. A. 31:1695-1697.
29. Jain, M. K., and L. V. Wray, Jr. 1977. Partition coefficients of alkanols in lipid bilayer/water. Biochem. Pharma. 27:1294-1296.
30. Katz, Y., and J. M. Diamond. 1974. Thermodynamic constants for nonelectrolyte partition between dimyristoyl lecithin and water. J. Membr. Biol. 17:101-120.
31. Katz, Y., M. E. Hoffman, and R. Blumenthal. 1983. Parametric analysis of membrane characteristics and membrane structure. J. Theor. Biol. 105:493-510.
32. Koubi, L., M. Tarek, M. L. Klein, and D. Scharf. 2000. Distribution of halothane in a dipalmitoylphosphatidylcholine bilayer from molecular dynamics calculations. Biophys. J. 78:800-811.
33. Lande, M. B., J. M. Donovan, and M. L. Zeidel. 1995. The relationship between membrane fluidity and permeabilities to water, solutes, ammonia and protons. J. Gen. Physiol. 106:67-84.
34. Lieb, W. R., and W. D. Stein. 1969. Biological membranes behave as non-porous polymeric sheets with respect to the diffusion of non-electrolytes. Nature. 224:240-243.
35. Lieb, W. R., and W. D. Stein. 1971. The molecular basis of simple diffusion within biological membranes. Curr. Top. Membr. Transp. 2:1-39.
36. MacKerell, A. D., and S. E. Feller. 2000. An improved empirical potential energy function for molecular simulations of phospholipids. J. Phys. Chem. B. 104:7510-7515.
37. Marqusee, J. A., and K. A. Dill. 1986. Solute partitioning into chain molecule interphases: monolayers, bilayers membranes and micelles. J. Chem. Phys. 85:434-444.
38. Marrink, S. J., and H. J. C. Berendsen. 1994. Simulation of water transport through a lipid-membrane. J. Phys. Chem. 98:4155-4168.
39. Marrink, S. J., and H. J. C. Berendsen. 1996. Permeation process of small molecules across lipid membranes studied by molecular dynamics simulations. J. Phys. Chem. 100:16729-16738.
40. Marrink, S. J., R. M. Sok, and H. J. C. Berendsen. 1996. Free volume properties of a simulated lipid membrane. J. Chem. Phys. 104:9090-9099.
41. Nagle, J. F., and S. Tristram-Nagle. 2000. Structure of lipid bilayers. Biochim. Biophys. Acta. Rev. Biomembr. 1469:159-195.
42. Nagle, J. R., R. Zhang, S. Tristram-Nagle, W. Sun, H. Petrache, and R. M. Suter. 1996. X-ray structure determination of fully hydrated Lα-phase dipalmitoylphosphatidylcholine bilayers. Biophys. J. 70:1419-1431.
43. Orbach, E., and A. Finkelstein. 1980. The nonelectrolyte permeability of planar lipid bilayer membranes. J. Gen. Physiol. 75:427-436.
44. Overton, E. 1895. Uber die osmotischen eigenshaften der lebenden pflanzen und tierzellen. Vierteljahrschr. Naturforsch. Ges. Zurich. 40:159-201.
45. 1 relaxation in lipid bilayer vesicles. J. Chem. Phys. 89:1128-1140.
46. Paula, S., A. G. Volkov, A. N. Van Hoek, T. H. Haines, and D. W. Deamer. 1996. Permeation of protons, potassium ions, and small polar molecules through phospholipid bilayers as a function of membrane thickness. Biophys. J. 70:339-348.
47. Pohorille, A., M. H. New, K. Schweighofer, and M. A. Wilson. 1999. Insights from computer simulations into the interaction of small molecules with lipid bilayers. Curr. Top. Membr. 48:49-76.
48. Pohorille, A., and M. A. Wilson. 1996. Excess chemical potential of small solutes across water-membrane and water-hexane interfaces. J. Chem. Phys. 104:3760-3773.
49. Pratt, L. R., and A. Pohorille. 2002. Hydrophobic effects and modeling of biophysical aqueous solution interfaces. Chem. Rev. 102:2671-2692.
50. Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comp. Phys. 23:327-341.
51. Seelig, J. 1977. Deuterium magnetic resonance: theory and application to lipid membranes. Q. Rev. Biophys. 10:353-418.
52. Simon, S. A., and J. Gutknecht. 1980. Solubility of carbon dioxide in lipid bilayer membranes and organic solvents. Biochim. Biophys. Acta. 596:352-358.
53. Simon, S. A., W. L. Stone, and P. B. Bennet. 1979. Can regular solution theory be applied to lipid bilayer membranes? Biochim. Biophys. Acta. 550:38-47.
54. Simon, S. A., W. L. Stone, and P. Busto-Latorre. 1977. A thermodynamic study of the partition of n-hexane into phosphatidylcholine and phosphatidylcholine-cholesterol bilayers. Biochim. Biophys. Acta. 468:378-388.
55. Singer, S., and G. L. Nicolson. 1972. The fluid mosaic model of cell membranes. Science. 172:720-730.
56. Smith, R. A., E. G. Porter, and K. W. Miller. 1981. The solubility of anesthetic gases in lipid bilayers. Biochim. Biophys. Acta. 645:327-338.
57. Stein, W. D. 1981. Permeability for lipophilic molecules. In Membrane Transport. S. L. Bonting and J. H. M. de Pont, editors. Elsevier/North-Holland Biomedical, New York.
58. Stone, W. L. 1975. Hydrophobic interaction of alkanes with liposomes and lipoproteins. J. Biol. Chem. 250:4368-4370.
59. Stouch, T. R., H. E. Alper, and D. Bassolino. 1995. Simulations of drug diffusion in biomembranes. Comp. Aided Mol. Des. 589:127-138.
60. Todd, A. P., R. J. Mehlhom, and R. I. Macey. 1989. Amine and carboxylate spin probe permeability in red cells. J. Membr. Biol. 109:41-52.
61. Tu, K., M. Tarek, M. L. Klein, and D. Scharf. 1998. Effects of anesthetics on the structure of a phospholipid bilayer: molecular dynamics investigation of halothane in the hydrated liquid crystal phase of dipalmitoylphosphatidylcholine. Biophys. J. 75:2123-2134.
62. Venable, R. M., Y. Zhang, B. J. Hardy, and R. W. Pastor. 1993. Molecular dynamics simulations of a lipid bilayer and of hexadecane: an investigation of membrane fluidity. Science. 262:223-226.
63. Walter, A., and J. Gutknecht. 1984. Monocarboxylic acid permeation through lipid bilayer membranes. J. Membr. Biol. 77:255-264.
64. Walter, A., and J. Gutknecht. 1986. Permeability of small nonelectrolytes through lipid bilayer membranes. J. Membr. Biol. 90:207-217.
65. Wolosin, J. M., and H. Ginsburg. 1975. The permeation of organic acids through lecithin bilayers resemblance to diffusion in polymers. Biochim. Biophys. Acta. 389:20-33.
66. Wolosin, J. M., H. Ginsburg, W. R. Lieb, and W. D. Stein. 1978. Diffusion within egg-lecithin bilayers resembles that within soft polymers. J. Gen. Physiol. 71:93-100.
67. Xiang, T. X. 1998. A novel dynamic free-volume theory for molecular diffusion in fluids and interphases. J. Chem. Phys. 109:7876-7884.
68. Xiang, T. X. 1999. Translational diffusion in lipid bilayers: dynamic free-volume theory and molecular dynamics simulation. J. Phys. Chem. B. 103:385-394.
69. Xiang, T. X., and B. D. Anderson. 1994. The relationship between permeant size and permeability in lipid bilayer membranes. J. Membr. Biol. 140:111-122.
70. Xiang, T. X., and B. D. Anderson. 1995. Phospholipid surface density determines the partitioning and permeability of acetic acid in DMPC:Cholesterol bilayers. J. Membr. Biol. 148:157-167.
71. Xiang, T. X., and B. D. Anderson. 1997. Permeability of acetic acid across gel and liquid-crystalline lipid bilayers conforms to free-surface-area theory. Biophys. J. 72:223-237.
72. Xiang, T. X., and B. D. Anderson. 1998a. The barrier domain for solute permeation varies with lipid bilayer phase structure. J. Membr. Biol. 165:77-90.
73. Xiang, T. X., and B. D. Anderson. 1998b. Influence of chain ordering on the selectivity of dipalmitoylphosphatidylcholine bilayer membranes for permeant size and shape. Biophys. J. 75:2658-2671.
74. Xiang, T. X., and B. D. Anderson. 1998c. Phase structure of binary lipid bilayers as revealed by permeability of small molecules. Biochim. Biophys. Acta. 1370:64-76.
75. Xiang, T. X., and B. D. Anderson. 2000a. Influence of a transmembrane protein on the permeability of small molecules across lipid membranes. J. Membr. Biol. 173:187-201.
76. Xiang, T. X., and B. D. Anderson. 2000b. A quantitative model for the dependence of solute permeability on peptide and cholesterol content in biomembranes. J. Membr. Biol. 177:137-148.
77. Xiang, T. X., X. Chen, and B. D. Anderson. 1992. Transport methods for probing the barrier domain of lipid bilayer membranes. Biophys. J. 63: 78-88.
78. 2 atomic charges. J. Chem. Phys. 109:9117-9133.