Skip to main content
NCBI home page
Biophysical Journal logoLink to Biophysical Journal
. 1999 Nov;77(5):2462–2469. doi: 10.1016/S0006-3495(99)77082-7

Combined monte carlo and molecular dynamics simulation of fully hydrated dioleyl and palmitoyl-oleyl phosphatidylcholine lipid bilayers

SW Chiu 1, E Jakobsson 1, S Subramaniam 1, HL Scott 1
PMCID: PMC1300522  PMID: 10545348

Abstract

We have applied a new equilibration procedure for the atomic level simulation of a hydrated lipid bilayer to hydrated bilayers of dioleyl-phosphatidylcholine (DOPC) and palmitoyl-oleyl phosphatidylcholine (POPC). The procedure consists of alternating molecular dynamics trajectory calculations in a constant surface tension and temperature ensemble with configurational bias Monte Carlo moves to different regions of the configuration space of the bilayer in a constant volume and temperature ensemble. The procedure is applied to bilayers of 128 molecules of POPC with 4628 water molecules, and 128 molecules of DOPC with 4825 water molecules. Progress toward equilibration is almost three times as fast in central processing unit (CPU) time compared with a purely molecular dynamics (MD) simulation. Equilibration is complete, as judged by the lack of energy drift in 200-ps runs of continuous MD. After the equilibrium state was reached, as determined by agreement between the simulation volume per lipid molecule with experiment, continuous MD was run in an ensemble in which the lateral area was restrained to fluctuate about a mean value and a pressure of 1 atm applied normal to the bilayer surface. Three separate continuous MD runs, 200 ps in duration each, separated by 10,000 CBMC steps, were carried out for each system. Properties of the systems were calculated and averaged over the three separate runs. Results of the simulations are presented and compared with experimental data and with other recent simulations of POPC and DOPC. Analysis of the hydration environment in the headgroups supports a mechanism by which unsaturation contributes to reduced transition temperatures. In this view, the relatively horizontal orientation of the unsaturated bond increases the area per lipid, resulting in increased water penetration between the headgroups. As a result the headgroup-headgroup interactions are attenuated and shielded, and this contributes to the lowered transition temperature.

Full Text

The Full Text of this article is available as a PDF (843.0 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Armen R. S., Uitto O. D., Feller S. E. Phospholipid component volumes: determination and application to bilayer structure calculations. Biophys J. 1998 Aug;75(2):734–744. doi: 10.1016/S0006-3495(98)77563-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Berde C. B., Andersen H. C., Hudson B. S. A theory of the effects of head-group structure and chain unsaturation on the chain melting transition of phospholipid dispersions. Biochemistry. 1980 Sep 2;19(18):4279–4293. doi: 10.1021/bi00559a021. [DOI] [PubMed] [Google Scholar]
  3. Berger O., Edholm O., Jähnig F. Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophys J. 1997 May;72(5):2002–2013. doi: 10.1016/S0006-3495(97)78845-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Chiu S. W., Clark M., Balaji V., Subramaniam S., Scott H. L., Jakobsson E. Incorporation of surface tension into molecular dynamics simulation of an interface: a fluid phase lipid bilayer membrane. Biophys J. 1995 Oct;69(4):1230–1245. doi: 10.1016/S0006-3495(95)80005-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Egberts E., Marrink S. J., Berendsen H. J. Molecular dynamics simulation of a phospholipid membrane. Eur Biophys J. 1994;22(6):423–436. doi: 10.1007/BF00180163. [DOI] [PubMed] [Google Scholar]
  6. Feller S. E., Yin D., Pastor R. W., MacKerell A. D., Jr Molecular dynamics simulation of unsaturated lipid bilayers at low hydration: parameterization and comparison with diffraction studies. Biophys J. 1997 Nov;73(5):2269–2279. doi: 10.1016/S0006-3495(97)78259-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Hristova K., White S. H. Determination of the hydrocarbon core structure of fluid dioleoylphosphocholine (DOPC) bilayers by x-ray diffraction using specific bromination of the double-bonds: effect of hydration. Biophys J. 1998 May;74(5):2419–2433. doi: 10.1016/S0006-3495(98)77950-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Huang P., Perez J. J., Loew G. H. Molecular dynamics simulations of phospholipid bilayers. J Biomol Struct Dyn. 1994 Apr;11(5):927–956. doi: 10.1080/07391102.1994.10508045. [DOI] [PubMed] [Google Scholar]
  9. Jakobsson E. Computer simulation studies of biological membranes: progress, promise and pitfalls. Trends Biochem Sci. 1997 Sep;22(9):339–344. doi: 10.1016/s0968-0004(97)01096-7. [DOI] [PubMed] [Google Scholar]
  10. Nagle J. F., Wiener M. C. Structure of fully hydrated bilayer dispersions. Biochim Biophys Acta. 1988 Jul 7;942(1):1–10. doi: 10.1016/0005-2736(88)90268-4. [DOI] [PubMed] [Google Scholar]
  11. Nagle J. F., Zhang R., Tristram-Nagle S., Sun W., Petrache H. I., Suter R. M. X-ray structure determination of fully hydrated L alpha phase dipalmitoylphosphatidylcholine bilayers. Biophys J. 1996 Mar;70(3):1419–1431. doi: 10.1016/S0006-3495(96)79701-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Petrache H. I., Feller S. E., Nagle J. F. Determination of component volumes of lipid bilayers from simulations. Biophys J. 1997 May;72(5):2237–2242. doi: 10.1016/S0006-3495(97)78867-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Seelig J., Waespe-Sarcevic N. Molecular order in cis and trans unsaturated phospholipid bilayers. Biochemistry. 1978 Aug 8;17(16):3310–3315. doi: 10.1021/bi00609a021. [DOI] [PubMed] [Google Scholar]
  14. Tieleman D. P., Marrink S. J., Berendsen H. J. A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. Biochim Biophys Acta. 1997 Nov 21;1331(3):235–270. doi: 10.1016/s0304-4157(97)00008-7. [DOI] [PubMed] [Google Scholar]
  15. Tristram-Nagle S., Petrache H. I., Nagle J. F. Structure and interactions of fully hydrated dioleoylphosphatidylcholine bilayers. Biophys J. 1998 Aug;75(2):917–925. doi: 10.1016/S0006-3495(98)77580-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Tu K., Tobias D. J., Klein M. L. Constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine bilayer. Biophys J. 1995 Dec;69(6):2558–2562. doi: 10.1016/S0006-3495(95)80126-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Venable R. M., Zhang Y., Hardy B. J., Pastor R. W. Molecular dynamics simulations of a lipid bilayer and of hexadecane: an investigation of membrane fluidity. Science. 1993 Oct 8;262(5131):223–226. doi: 10.1126/science.8211140. [DOI] [PubMed] [Google Scholar]
  18. Wiener M. C., White S. H. Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of x-ray and neutron diffraction data. II. Distribution and packing of terminal methyl groups. Biophys J. 1992 Feb;61(2):428–433. doi: 10.1016/S0006-3495(92)81848-9. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Biophysical Journal are provided here courtesy of The Biophysical Society

RESOURCES