Simulations of biomembranes and water: Important technical aspects

Fluid Phase Equilibria

Volumn 261, Issue 1-2, 2007, Pages 18-25

  Bennun, Sandra V ^a   Dickey, Allison N ^a   Xing, Chenyue ^a   Faller, Roland ^a  

^a University of California Davis   (United States)

Author keywords

Biomembranes; Molecular simulation

Indexed keywords

ALCOHOLS; ANISOTROPY; COMPUTER SIMULATION; MOLECULAR MODELING; PHASE BEHAVIOR; SURFACE TENSION; WATER;

BILAYER SIMULATIONS; BIOMEMBRANES; DRAMATIC REPERCUSSIONS; TECHNICAL ASPECTS;

BIOLOGICAL MEMBRANES;

ALCOHOLS; ANISOTROPY; BIOLOGICAL MEMBRANES; COMPUTER SIMULATION; MOLECULAR MODELING; PHASE BEHAVIOR; SURFACE TENSION; WATER;

EID: 35348845092     PISSN: 03783812     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.fluid.2007.07.056     Document Type: Article

References (50)

1. Egberts E., Marrink S.-J., and Berendsen H.J.C. Eur. Biophys. J. Molecular dynamics simulation of a phospholipid membrane 22 6 (1994) 423-436
2. Tieleman D.P., Marrink S.J., and Berendsen H.J.C. A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. Biochim. Biophys. Acta (Rev. Biomem.) 1331 3 (1997) 235-270
3. Sum A.K., Faller R., and de Pablo J.J. Molecular simulation study of phospholipid bilayers and insights of the interactions with disaccharides. Biophys. J. 85 5 (2003) 2830-2844
4. Faller R., and Marrink S.-J. Simulation of domain formation in mixed DLPC-DSPC lipid bilayers. Langmuir 20 18 (2004) 7686-7693
5. Lee B.W., et al. Structural effects of small molecules on phospholipid bilayers investigated by molecular simulations. Fluid Phase Equilib. 225 (2004) 63-68
6. Switzer J., et al. Karhunen-Loeve analysis for pattern description in phase separated lipid bilayer systems. J. Chem. Phys. 124 23 (2006) 234906
7. Cooke I.R., Kremer K., and Deserno M. Tunable generic model for fluid bilayer membranes. Phys. Rev. E 72 1 (2005) 0115061
8. Moore P.B., Lopez C.F., and Klein M.L. Dynamical properties of a hydrated lipid bilayer from a multinanosecond molecular dynamics simulation. Biophys. J. 81 5 (2001) 2484-2494
9. Lopez C.F., et al. Self-assembly of a phospholipid Langmuir monolayer using coarse-grained molecular dynamics simulations. J. Phys. Condens. Matter 14 (2002) 9431-9444
10. Patra M., et al. Lipid bilayers driven to a wrong plane in molecular dynamics simulations by truncation of long-range electrostatic interactions. J. Phys. Chem. B 108 14 (2004) 4485-4494
11. Feller S.E., et al. Effect of electrostatic force truncation on interfacial and transport properties of water. J. Phys. Chem. 100 42 (1996) 17011-17020
12. Anezo C., et al. Methodological issues in lipid bilayer simulations. J. Phys. Chem. B 107 35 (2003) 9424-9433
13. Vega C., et al. Can simple models describe the phase diagram of water?. J. Phys. Condens. Matter 17 (2005) S3283-S3288
14. Berendsen H.J.C., et al. In: Pullman B. (Ed). Intermolecular Forces (1981), Reidel, Dordrecht 331-342
15. Berendsen H.J.C., Grigera J.R., and Straatsma T.P. The missing term in effective pair potentials. J. Phys. Chem. 91 24 (1987) 6269-6271
16. Jorgensen W.L., et al. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79 (1983) 926-935
17. Horn H.W., Swope W.C., and Pitera J.W. Characterization of the TIP4P-Ew water model: vapor pressure and boiling point. J. Chem. Phys. 123 19 (2005) 194504
18. Mahoney M.W., and Jorgensen W.L. A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. J. Chem. Phys. 112 (2000) 8910-8922
19. Farago O. Water-free computer model for fluid bilayer membranes. J. Chem. Phys. 119 1 (2003) 596-605
20. Marrink S.J., de Vries A.H., and Mark A.E. Coarse grained model for semi-quantitative lipid simulation. J. Phys. Chem. B 108 2 (2004) 750-760
21. Stevens M.J. Coarse-grained simulations of lipid bilayers. J. Chem. Phys. 121 (2004) 11942-11948
22. Shelley J.C., et al. A coarse grain model for phospholipid simulations. J. Phys. Chem. B 105 19 (2001) 4464-4470
23. Kaznessis Y.N., Kim S.T., and Larson R.G. Simulations of zwitterionic and anionic phospholipid monolayers. Biophys. J. 82 4 (2002) 1731-1742
24. Alper H.E., Bassolino D., and Stouch T.R. Computer simulation of a phospholipid monolayer-water system: the influence of long-range forces on water structure and dynamics. J. Chem. Phys. 98 12 (1993) 9798-9807
25. Feller S.E., Zhang Y.H., and Pastor R.W. Computer-simulation of liquid/liquid interfaces. II. Surface-tension area dependence of a bilayer and a monolayer. J. Chem. Phys. 103 23 (1995) 10267-10276
26. Sackmann E. Supported membranes: scientific and practical applications. Science 271 5245 (1996) 43-48
27. Sackmann E., and Tanaka M. Supported membranes on soft polymer cushions: fabrication. characterization and applications. Trends Biotechnol. 18 2 (2000) 58-64
28. Ratto T.V., and Longo M.L. Obstructed diffusion in phase-separated supported lipid bilayers: a combined atomic force microscopy and fluorescence recovery after photobleaching approach. Biophys. J. 83 6 (2002) 3380-3392
29. Groves J.T., and Boxer S.G. Micropattern formation in supported lipid membranes. Acc. Chem. Res. 35 3 (2002) 149-157
30. Lenz P., Ajo-Franklin C.M., and Boxer S.G. Patterned supported lipid bilayers and monolayers on poly(dimethylsiloxane). Langmuir 20 25 (2004) 11092-11099
31. Lin W., et al. Lipid asymmetry in DLPC/DSPC supported lipid bilayers: a combined AFM and fluorescence microscopy study. Biophys. J. 90 (2006) 228-237
32. Scott H.L. Modeling the lipid component of membranes. Curr. Opin. Struct. Biol. 12 4 (2002) 495-502
33. Kranenburg M., Vlaar M., and Smit B. Simulating induced interdigitation in membranes. Biophys. J. 87 (2004) 1596-1605
34. Simon S.A., and McIntosh T.J. Interdigitated hydrocarbon chain packing causes the biphasic transition behavior in lipid/alcohol suspensions. Biochim. Biophys. Acta 773 (1984) 169-172
35. Lindahl E., Hess B., and Spoel D.v.d. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. 7 8 (2001) 306-317
36. Berendsen H.J.C., et al. Molecular dynamics with coupling to an external heat bath. J. Chem. Phys. 81 8 (1984) 3684-3690
37. D.M. Heyes, The Liquid State: Applications of Molecular Simulations, Wiley, New York, 1998.
38. Bennun S.V., Longo M.L., and Faller R. Phase and mixing behavior in two-component lipid bilayers: a molecular dynamics study in DLPC/DSPC mixtures. J. Phys. Chem., B 111 32 (2007) 9504-9512
39. Kumar P., et al. Thermodynamics, structure, and dynamics of water confined between hydrophobic plates. Phys. Rev. E 72 5 (2005) 051503
40. D.P. Tieleman, University of Calgary, Department of Biological Sciences. http://moose.bio.ucalgary.ca/download.html.
41. Gunsteren W.F.v., et al. Biomolecular Simulation: The GROMOS Manual and User Guide (1996), Vdf, Zürich
42. Nath S.K., Banaszak B.J., and de Pablo J.J. A new united atom force field for α-olefins. J. Chem. Phys. 114 8 (2001) 3612-3616
43. Dickey A.N., and Faller R. How alcohol chain-length and concentration modulate hydrogen bond formation in a lipid bilayer. Biophys. J. 92 7 (2007) 2366-2376
44. Hess B., et al. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. 18 12 (1997) 1463-1472
45. Essman U., Perela L., Berkowitz M.L., Darden H.L.T., and Pedersen L.G. A smooth particle mesh Ewald method. J. Chem. Phys. 103 (1995) 8577-8592
46. Chiu S.W., Clark M., Balaji V., Subramaniam S., Scott H.L., and Jakobsson E. Incorporation of surface tension into molecular dynamics simulation of an interface: a fluid phase lipid bilayer membrane. Biophys. J. 69 (1995) 1230-1245
47. DeYoung L.R., and Dill K.A. Solute partitioning into lipid bilayer membranes. Biochemistry 27 (1988) 5281-5289
48. Nagle J.F., et al. X-ray structure determination of fully hydrated L(α) phase dipalmitoylphosphatidylcholine bilayers. Biophys. J. 70 3 (1996) 1419-1431
49. Tieleman D.P., and Berendsen H.J.C. Molecular dynamics simulations of fully hydrated dipalmitoylphosphatidylcholine bilayer with different macroscopic boundary conditions and parameters. J. Chem. Phys. 105 11 (1996) 4871-4880
50. Douliez J.P., Leonard A., and Dufourc E.J. Restatement of order parameters in biomembranes: calculation of C-C bond order parameters from C-D quadrupolar splittings. Biophys. J. 68 (1995) 1727-1739