Molecular Dynamics Simulation of a Palmitoyl-Oleoyl Phosphatidylserine Bilayer with Na+ Counterions and NaCl

Biophysical Journal

Volumn 86, Issue 3, 2004, Pages 1601-1609

  Mukhopadhyay, Parag ^a   Monticelli, Luca ^a,b   Tieleman, D Peter ^a  

^a UNIVERSITY OF CALGARY   (Canada)

^b UNIVERSITY OF MILAN   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

OXYGEN; PALMITOYLOLEOYLPHOSPHATIDYLSERINE; PHOSPHATIDYLSERINE; PHOSPHOLIPID; SODIUM CHLORIDE; SODIUM ION; UNCLASSIFIED DRUG; WATER;

ARTICLE; CHEMICAL STRUCTURE; COMPUTER GRAPHICS; HYDROGEN BOND; LIPID BILAYER; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR MODEL; PHOSPHOLIPID BILAYER;

EID: 1542285301     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(04)74227-7     Document Type: Article

References (42)

1. Anézo, C., A. H. de Vries, H.-D. Höltje, D. P. Tieleman, and S. J. Marrink. 2003. Methodological issues in lipid bilayer simulations. J. Phys. Chem. B. 107:9424-9433.
2. Berendsen, H. J. C., J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. Haak. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:3684-3690.
3. Berendsen, H. J. C., J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. 1981. Interaction models for water in relation to protein hydration. In Intermolecular Forces. B. Pullman, editor. Reidel, Dordrecht. 331-342.
4. Berendsen, H. J. C., D. van der Spoel, and R. van Drunen. 1995. GROMACS-a message-passing parallel molecular-dynamics implementation. Comput. Phys. Commun. 91:43-56.
5. Berger, O., O. Edholm, and F. Jähnig. 1997. Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophys. J. 72:2002-2013.
6. Böckmann, R. A., A. Hac, T. Heimburg, and H. Grubmüller. 2003. Effect of sodium chloride on a lipid bilayer. Biophys. J. 85:1647-1655.
7. Cascales, J. J. L., J. G. de la Torre, S. J. Marrink, and H. J. C. Berendsen. 1996. Molecular dynamics simulation of a charged biological membrane. J. Chem. Phys. 104:2713-2720.
8. Collins, K. D. 1997. Charge density-dependent strength of hydration and biological structure. Biophys. J. 72:65-76.
9. Darden, T., D. York, and L. Pedersen. 1993. Particle mesh Ewald-an N.Log(N) method for Ewald sums in large systems. J. Chem. Phys. 98:10089-10092.
10. Epand, R. M. 1998. Lipid polymorphism and protein-lipid interactions. Biochim. Biophys. Acta. 1376:353-368.
11. Essmann, U., L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen. 1995. A smooth particle mesh Ewald method. J. Chem. Phys. 103:8577-8593.
12. Gambu, I., and B. Roux. 1997. Interaction of K+ with a phospholipid bilayer: a molecular dynamics study. J. Phys. Chem. B. 101:6066-6072.
13. Grossfield, A., R. Pengyu, and J. W. Ponder. 2003. Ion solvation thermodynamics from simulation with a polarizable force field. J. Am. Chem. Soc. 125:15671-15682.
14. Hauser, H., and G. Poupart. 1992. Lipid structure. In The structure of biological membranes. P. Yeagle, editor. CRC Press, Boca Raton, FL. 3-71.
15. Hess, B., H. Bekker, H. J. C. Berendsen, and J. Fraaije. 1997. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. 18:1463-1472.
16. Hockney, R. W., S. P. J. Goel, and J. W. Eastwood. 1974. Quite high resolution computer models of a plasma, J. Comput. Phys. 14:148-158.
17. Humphrey, W., A. Dalke, and K. Schulten. 1996. VMD: visual molecular dynamics, J. Mol. Graph. 14:33-38.
18. Lindahl, E., and O. Edholm. 2000. Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations, Biophys. J. 79:426-433.
19. Lindahl, E., B. Hess, and D. van der Spoel. 2001. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. 7:306-317.
20. Luzzati, V. 1997. Biological significance of lipid polymorphism: the cubic phases. Curr. Opin. Struct. Biol. 7:661-668.
21. Marrink, S. J., E. Lindahl, O. Edholm, and A. E. Mark. 2001. Simulation of the spontaneous aggregation of phospholipids into bilayers. J. Am. Chem. Soc. 123:8638-8639.
22. Mashl, R. J., H. L. Scott, S. Subramaniam, and E. Jakobsson. 2001. Molecular simulation of dioleoylphosphatidylcholine lipid bilayers at differing levels of hydration. Biophys. J. 81:3005-3015.
23. Matsuzaki, K. 1998. Magainins as paradigm for the mode of action of pore forming polypeptides. Biochim. Biophys. Acta. 1376:391-400.
24. Matsuzaki, K. 1999. Why and how are peptide-lipid interactions utilized for self-defense? Magainins and tachyplesins as archetypes. Biochim. Biophys. Acta. 1462:1-10.
25. Mattai, J., H. Hauser, R. A. Demel, and G. G. Shipley. 1989. Interactions of metal ions with phosphatidylserine bilayer membrane: effect of hydrocarbon chain unsaturation. Biochemistry. 28:2322-2330.
26. Miyamoto, S., and P. A. Kollman. 1992. SETTLE-an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J. Comput. Chem. 13:952-962.
27. Mukhopadhyay, P., H. J. Vogel, and D. P. Tieleman. 2004. Distribution of pentachlorophenol in phospholipid bilayers: A molecular dynamics study. Biophys. J. 86:337-345.
28. Murzyn, K., T. Rog, G. Jezierski, Y. Takaoka, and M. Pasenkiewicz-Gierula. 2001. Effects of phospholipid unsaturation on the membrane/water interface: a molecular simulation study. Biophys. J. 81:170-183.
29. Nagle, J. F., and S. Tristram-Nagle. 2000. Structure of lipid bilayers. Biochim. Biophys. Acta. 1469:159-195.
30. Pandit, S. A., and M. L. Berkowitz. 2002. Molecular dynamics simulation of dipalmitoylphosphatidylserine bilayer with Na+ counterions. Biophys. J. 82:1818-1827.
31. Pandit, S. A., D. Bostick, and M. L. Berkowitz. 2003a. An algorithm to describe molecular scale surface and its application to the study of a water/lipid bilayer interface. J. Chem. Phys. 119:2199-2205.
32. Pandit, S. A., D. Bostick, and M. L. Berkowitz. 2003b. Molecular dynamics simulation of a dipalmitoylphosphatidylcholine bilayer with NaCl. Biophys. J. 84:3743-3750.
33. Petrache, H. I., K. C. Tu, and J. F. Nagle. 1999. Analysis of simulated NMR order parameters for lipid bilayer structure determination. Biophys. J. 76:2479-2487.
34. Petrache, H. I., S. E. Feller, and J. F. Nagle. 1997. Determination of component volumes of lipid bilayers from simulations. Biophys. J. 70:2237-2242.
35. Petrache, H. I., S. Tristram-Nagle, K. Gawrisch, D. Harries, V. A. Parsegian, and J. F. Nagle. 2004. Structure and fluctuations of charged phosphatidylserine bilayers in the absence of salt. Biophys. J. 86:1574-1586.
36. Sachs, J. N., and T. B. Woolf. 2003. Understanding the Hofmeister effect in interactions between chaotropic anions and lipid bilayers: molecular dynamics simulation. J. Am. Chem. Soc. 125:8742-8743.
37. Saiz, L., and M. L. Klein. 2001. Structural properties of a highly polyunsaturated lipid bilayer from molecular dynamics simulations. Biophys. J. 81:204-216.
38. Saiz, L., and M. L. Klein. 2002. Computer simulation studies of model biological membranes. Acc. Chem. Res. 35:482-489.
39. Scott, H. L. 2002. Modeling the lipid component of membranes. Curr. Opin. Struct. Biol. 12:495-502.
40. Tieleman, D. P., S. J. Marrink, and H. J. C. Berendsen. 1997. A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. Biochim. Biophys. Acta. 1331:235-270.
41. van Gunsteren, W. F., P. Kruger, S. R. Billeter, A. E. Mark, A. A. Eising, W. R. P. Scott, P. H. Huneberg, and I. G. Tironi. 1996. Biomolecular Simulation: The GROMOS96 Manual and User Guide. Biomos Hochschulverlag AG an der ETH Zurich, Groningen, Germany.
42. van Klompenburg, W., I. Nilsson, G. von Heijne, and B. de Kruijff. 1997. Anionic phospholipids are determinants of membrane protein topology. EMBO J. 16:4261-4266.