Molecular Dynamics Simulation of the Spontaneous Formation of a Small DPPC Vesicle in Water in Atomistic Detail

Journal of the American Chemical Society

Volumn 126, Issue 14, 2004, Pages 4488-4489

  De Vries, Alex H ^a   Mark, Alan E ^a   Marrink, Siewert J ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

DIPALMITOYLPHOSPHATIDYLCHOLINE; WATER;

ARTICLE; ATOM; BILAYER MEMBRANE; FORCE; HYDRATION; MEMBRANE TRANSPORT; MICELLE; MOLECULAR DYNAMICS; PHOSPHOLIPID VESICLE; POROSITY; SIMULATION; STOICHIOMETRY;

1,2-DIPALMITOYLPHOSPHATIDYLCHOLINE; COMPUTER SIMULATION; LIPOSOMES; MODELS, CHEMICAL; THERMODYNAMICS; WATER;

EID: 1842738717     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0398417     Document Type: Article

References (20)

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9. Simulations were performed using isotropic pressure (P = 1 bar) conditions at T = 323 K with the force field as described for system F in: Anézo, C.; de Vries, A. H.; Höltje, H.-D.; Tieleman, D. P.; Marrink, S. J. J. Phys. Chem. B 2003, 107, 9424-9433, with a long-range cutoff of 1.5 nm, using a reaction-field correction and periodic boundary conditions. All simulations were performed with the GROMACS code (Lindahl, E.; Hess, B.; van der Spoel, D. J. Mol. Model. 2001, 7, 306-317) on a cluster of 1.7 GHz Intel Pentium IV processors. The code was run in parallel on four or eight processors under MPI. The rate of simulation was 1 ps per processor CPU hour.
10. Simulations were performed using isotropic pressure (P = 1 bar) conditions at T = 323 K with the force field as described for system F in: Anézo, C.; de Vries, A. H.; Höltje, H.-D.; Tieleman, D. P.; Marrink, S. J. J. Phys. Chem. B 2003, 107, 9424-9433, with a long-range cutoff of 1.5 nm, using a reaction-field correction and periodic boundary conditions. All simulations were performed with the GROMACS code (Lindahl, E.; Hess, B.; van der Spoel, D. J. Mol. Model. 2001, 7, 306-317) on a cluster of 1.7 GHz Intel Pentium IV processors. The code was run in parallel on four or eight processors under MPI. The rate of simulation was 1 ps per processor CPU hour.
11. Marrink, S. J.; Lindahl, E.; Edholm, O.; Mark, A. E. J. Am. Chem. Soc. 2001, 123, 8638-8639.
12. Note, the formation of a (multi)lamellar system is not prohibited.
13. (a) Tieleman, D. P.; Leontiadou, H.; Mark, A. E.; Marrink, S. J. J. Am. Chem. Soc. 2003, 125, 6382-6383.
14. (b) Leontiadou, H.; Mark, A. E.; Marrink, S. J. Biophys. J. 2004, in press.
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16. (a) Cornell, B. A.; Fletcher, G. C.; Middlehurst, J.; Separovic, F. Biochim. Biophys. Acta 1982, 690, 15-19.
17. (b) Vesicles with a diameter of 13 nm have been observed for other amphiphiles: Buwalda, R. T.; Stuart, M. C. A.; Engberts, J. B. F. N. Langmuir 2002, 18, 6507-6512.
18. A simulation using the CG model of ref 3d with the same setup as used for the atomistic model resulted in a sealed vesicle containing 1012 lipids after 30 ns with intermediates similar to those shown here for the atomistic model.
19. The vesicular state at the end of the simulation is formed by 1002 DPPC lipids. The remaining 15 lipids formed a micelle during the simulation. The assignment of lipids to inner and outer leaflets is somewhat arbitrary because a number of headgroups are lining water pores and therefore do not clearly belong to either the inner or the outer leaflet.
20. First neighbor headgroups strongly favor antiparallel orientations, minimizing dipole-dipole repulsion. Second neighbors show a weak preference for parallel orientation. After the second shell of neighbors, the correlation disappears quickly.