Molecular Dynamics Simulations of DOPC Lipid Bilayers: The Effect of Lennard-Jones Parameters of Hydrocarbon Chains


The current Chemistry at Harvard Molecular Mechanics (CHARMM) force field cannot accurately describe the properties of unsaturated phospholipid membranes. In this paper, a series of simulations was performed in which the Lennard- Jones (L-J) parameters of lipid acyl chains of dioleoylphosphatidylcholine (DOPC) were systematically adjusted. The results showed that adjustment of the L-J parameters in lipid acyl chains can significantly improve the current CHARMM force field. It was found that the L-J parameters have different influences on the order parameters of the top half and bottom half of the chain, separated by the cis double bond. The order parameters of the top half and the bottom half of the chain are related to the area/lipid and the length of the chain, respectively.

Share and Cite:

A. Liu and X. Qi, "Molecular Dynamics Simulations of DOPC Lipid Bilayers: The Effect of Lennard-Jones Parameters of Hydrocarbon Chains," Computational Molecular Bioscience, Vol. 2 No. 3, 2012, pp. 78-82. doi: 10.4236/cmb.2012.23007.

Conflicts of Interest

The authors declare no conflicts of interest.


[1] P. K. J. Kinnunen, A. K?iv, J. Y. A. Lehtonen, M. Ryt?maa and P. Mustonen, “Lipid Dynamics and Peripheral Interactions of Proteins with Membrane Surfaces,” Chemistry and Physics of Lipids, Vol. 73, No. 1-2, 1994, pp. 181-207. doi:10.1016/0009-3084(94)90181-3
[2] M. Kobayashi, R. K. Nutharasan, J. W. Feng, M. F. Robert and J. W. Lomasney, “Identification of Hydro- phobic Interactions between Proteins and Lipids:? Free Fatty Acids Activate Phospholipase C δ1 via Allosterism,” Biochemistry, Vol. 43, No. 23, 2004,, pp. 7522-7533. doi:10.1021/bi035966c
[3] R. W. Benz, F. Castro-Román, D. J. Tobias and S. H. White, “Experimental Validation of Molecular Dynamics Simulations of Lipid Bilayers: A New Approach,” Biophysical Journal, Vol. 88, No. 2, 2005, pp. 805-817. doi:10.1529/biophysj.104.046821
[4] S. Berneche, M. Nina and B. Roux, “Molecular Dynamics Simulation of Melittin in a Dimyristoylphosphatidylcholine Bilayer Membrane,” Biophysical Journal, Vol. 75, No. 4, 1998, pp. 1603-1618. doi:10.1016/S0006-3495(98)77604-0
[5] S. Y. Bhide and M. L. Berkowitz, “Structure and Dynamics of Water at the Interface with Phospholipid Bilayers,” The Journal of Chemical Physics, Vol. 123, No. 22, 2005, pp. 224702.1-224702.16. doi:10.1063/1.2132277
[6] F. Castro-Román, R. W. Benz, S. H. White and D. J. Tobia, “Investigation of Finite System-Size Effects in Molecular Dynamics Simulations of Lipid Bilayers,” The Journal of Chemical Physics B, Vol. 110, No. 47, 2006, pp. 24157-24164. doi:10.1021/jp064746g
[7] S. E. Feller, R. M. Venable and R. W. Pastor, “Computer Simulation of a DPPC Phospholipid Bilayer:? Structural Changes as a Function of Molecular Surface Area,” Langmuir, Vol. 13, No. 24, 1997, pp. 6555-6561. doi:10.1021/la970746j
[8] S. E. Feller, D. Yin, R. W. Pastor and J. A. D. MacKerell, “Molecular Dynamics Simulation of Unsaturated Lipid Bilayers at Low Hydration: Parameterization and Comparison with Diffraction Studies,” Biophysical Journal, Vol. 73, No.5, 1997, pp. 2269-2279. doi:10.1016/S0006-3495(97)78259-6
[9] L. R. Forrest and M. S. P. Sansom, “Membrane simulations: bigger and better?” Current Opinion in Structural Biology, Vol. 10, No. 2, 2000, pp. 174-181. doi:10.1016/S0959-440X(00)00066-X
[10] P. Mukhopadhyay, L. Monticelli and D. P. Tieleman, “Molecular Dynamics Simulation of a Palmitoyl-Oleoyl Phosphatidylserine Bilayer with Na+ Counterions and NaCl,” Biophysical Journal, Vol. 86, No. 3, 2004, pp. 1601-1609. doi:10.1016/S0006-3495(04)74227-7
[11] B. Roux and T. B. Woolf, “Molecular Dynamics of Pf1 Coat Protein in a Phospholipid Bilayer,” In: K. M. Merz Jr. and B. Roux, Eds., Biological Membranes: A Molecular Perspective from Computation and Experiment, Birkhauser Press, Boston, 1996, pp. 555-587.
[12] D. J. Tobias, K. Tu and M. L. Klein, “Atomic-Scale Mo- lecular Dynamics Simulations of Lipid Membranes,” Current Opinion in Colloid & Interface Science,Vol. 2, No. 1, 1997, pp. 15-26. doi:10.1016/S1359-0294(97)80004-0
[13] S. W. Chiu, E. Jakobsson, S. Subramaniam and H. L. Scott, “Combined Monte Carlo and Molecular Dynamics Simulation of Fully Hydrated Dioleyl and Palmitoyloleyl Phosphatidylcholine Lipid Bilayers,” Biophysical Journal, Vol. 77, No. 5, 1999, pp. 2462-2469. doi:10.1016/S0006-3495(99)77082-7
[14] R. J. Mashl, H. L. Scott, S. Subramaniam and E. Jokobsson, “Molecular Simulation of Dioleoylphosphatidylcho- line Lipid Bilayers at Differing Levels of Hydration,” Biophysical Journal, Vol. 81, 2001, pp. 3005-3015. doi:10.1016/S0006-3495(01)75941-3
[15] E. A. Dolan, R. M. Venable, R. W. Pastor and B. R. Brooks, “Simulations of Membranes and Other Interfacial Systems Using P21 and Pc Periodic Boundary Conditions,” Biophysical Journal, Vol. 82, 2002, pp. 2317-2325. doi:10.1016/S0006-3495(02)75577-X
[16] S. E. Feller, Y. Zhang and R. W. Pastor, “Computer Simulation of Liquid/Liquid Interfaces. II. Surface Tension—Area Dependence of a Bilayer and Monolayer,” Journal of Chemical Physics, Vol. 103, No. 23, 1995, pp. 10267-10276. doi:10.1063/1.469928
[17] F. J?hnig, “What Is the Surface Tension of a Lipid Bilayer Membrane?” Biophysical Journal, Vol. 71, No. 3, 1996, pp. 1348-1349. doi:10.1016/S0006-3495(96)79336-0
[18] B. Roux, “Commentary: Surface Tension of Biomembranes,” Biophysical Journal, Vol. 71, No. 3, 1996, pp. 1346-1347. doi:10.1016/S0006-3495(96)79335-9
[19] R. Sankararamakrishman and H. Weinstein, “Surface Tension Parameterization in Molecular Dynamics Simulations of a Phospholipid-Bilayer Membrane:? Calibration and Effects,” The Journal of Chemical Physics B, Vol. 108, No. 31, 2004, pp. 11802-11811. doi:10.1021/jp048969n
[20] O. Berger, O. Edholm and F. J?hnig, “Molecular Dynamics Simulations of a Fluid Bilayer of Dipalmitoylphos- phatidylcholine at Full Hydration, Constant Pressure, and Constant Temperature,” Biophysical Journal, Vol. 72, No. 5, 1997, pp. 2002-2013. doi:10.1016/S0006-3495(97)78845-3
[21] S. E. Feller, Y. Zhang, R. W. Pastor and B. R. Brooks, “Constant Pressure Molecular Dynamics Simulation: The Langevin Piston Method,” The Journal of Chemical Physics, Vol. 103, No. 11, 1995, pp. 4613-4621. doi:10.1063/1.470648
[22] K. Tu, D. J. Tobias and M. L. Klein, “Constant Pressure and Temperature Molecular Dynamics Simulation of a Fully Hydrated Liquid Crystal Phase Dipalmitoylphosphatidylcholine Bilayer,” Biophysical Journal, Vol. 69, No. 6, 1995, pp. 2558-2562. doi:10.1016/S0006-3495(95)80126-8
[23] K. Tu, D. J. Tobias and M. L. Klein, “Constant Pressure and Temperature Molecular Dynamics Simulations of Crystals of the Lecithin Fragments: Glycerylphosphoryl- choline and Dilauroylglycerol,” The Journal of Chemical Physics, Vol. 99, No. 24, 1995, pp. 10035-10042. doi:10.1021/j100024a053
[24] A. A. Polyansky, P. E. Volynsky, D. E. Nolde, A. S. Arseniev and R. G. Efremov, The Journal of Chemical Physics B, Vol. 109, 2005, pp. 15052-15059.
[25] H. I. Petrache, S. Tristram-Nagle, K. Gawrisch, D. Harris, V. A. Parsegian and J. F. Nagle, “Structure and Fluctuations of Charged Phosphatidylserine Bilayers in the Absence of Salt,” Biophysical Journal, Vol. 86, No. 3, 2004, pp. 1574-1586. doi:10.1016/S0006-3495(04)74225-3
[26] M. C. Wiener and S. H. White, “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,” Biophysical Journal, Vol. 61, No. 2, 1992, pp. 428-433. doi:10.1016/S0006-3495(92)81848-9
[27] R. E. Jacobs and S. H. White, “The Nature of the Hydrophobic Binding of Small Peptides at the Bilayer Interface: Implications for the Insertion of Transbilayer Helices,” Biochemistry, Vol. 28, No. 8, 1989, pp. 3421-3437. doi:10.1021/bi00434a042
[28] B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan and M. Karplus, “CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations,” Journal of Computational Chemistry, Vol. 4, No. 2, 1983, pp. 187-217. doi:10.1002/jcc.540040211
[29] L. Kalé, R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan and K. Schulten, “NAMD2: Greater Scalability for Parallel Molecular Dynamics,” Journal of Computational Physics, Vol. 151, No. 1, 1999, pp. 283-312. doi:10.1006/jcph.1999.6201
[30] G. J. Martyna, D. J. Tobias and M. L. Klein, “Constant Pressure Molecular Dynamics Algorithms,” Journal of Chemical Physics, Vol. 101, No. 5, 1994, pp. 4177-4189. doi:10.1063/1.467468
[31] InsightII (San Diego, California, USA)

Copyright © 2021 by authors and Scientific Research Publishing Inc.

Creative Commons License

This work and the related PDF file are licensed under a Creative Commons Attribution 4.0 International License.