Validation of a hybrid MD-SCF coarse-grained model for DPPC in non-lamellar phases

  • Antonio De Nicola
  • Ying Zhao
  • Toshihiro Kawakatsu
  • Danilo Roccatano
  • Giuseppe Milano
Regular Article
Part of the following topical collections:
  1. Barone Festschrift Collection

Abstract

In the framework of a recently developed scheme for a hybrid particle-field simulation technique where self-consistent field theory and molecular dynamics simulation method are combined, specific coarse-grained models for aqueous solutions of phospholipids have been validated. In particular, the transferability of the model in the correct reproduction of non-lamellar phases has been validated against reference particle–particle simulations. By varying the water content, the proposed model is able to correctly describe the different morphologies that are experimentally observed such as micelles and reverse micelles. The lower computational costs of the hybrid techniques allow us to perform simulations of large-scale systems that are needed to investigate the applications of self-assembled structures of lipids in nanotechnologies.

Keywords

Coarse-graining Molecular dynamics Self-consistent field theory Lipids 

References

  1. 1.
    Bandyopadhyay S, Tarek M, Klein ML (1999) Molecular dynamics study of a lipid-DNA complex. J Phys Chem B 103(46):10075–10080. doi:10.1021/jp9927496 CrossRefGoogle Scholar
  2. 2.
    Saiz L, Klein ML (2002) Computer simulation studies of model biological membranes. Acc Chem Res 35(6):482–489. doi:10.1021/ar010167c CrossRefGoogle Scholar
  3. 3.
    Faller R, Marrink S-J (2004) Simulation of domain formation in DLPC-DSPC mixed bilayers. Langmuir 20(18):7686–7693. doi:10.1021/la0492759 CrossRefGoogle Scholar
  4. 4.
    Pal S, Milano G, Roccatano D (2006) Synthetic polymers and biomembranes. How do they interact?: Atomistic molecular dynamics simulation study of PEO in contact with a DMPC lipid bilayer. J Phys Chem B 110(51):26170–26179. doi:10.1021/jp063418d CrossRefGoogle Scholar
  5. 5.
    Bennett WFD, MacCallum JL, Hinner MJ, Marrink SJ, Tieleman DP (2009) Molecular view of cholesterol flip-flop and chemical potential in different membrane environments. J Am Chem Soc 131(35):12714–12720. doi:10.1021/ja903529f CrossRefGoogle Scholar
  6. 6.
    Katsaras J, Tristram-Nagle S, Liu Y, Headrick RL, Fontes E, Mason PC, Nagle JF (2000) Revisiting the ripple phase using fully hydrated, aligned DPPC multibilayers. Biophys J 78(1):20AGoogle Scholar
  7. 7.
    Ayton G, Smondyrev AM, Bardenhagen SG, McMurtry P, Voth GA (2002) Calculating the bulk modulus for a lipid bilayer with non-equilibrium molecular dynamics simulation. Biophys J 82:1226–1238CrossRefGoogle Scholar
  8. 8.
    Ayton G, Voth GA (2004) Mesoscopic lateral diffusion in lipid bilayers. Biophys J 87(5):3299–3311CrossRefGoogle Scholar
  9. 9.
    Ayton G, Voth GA (2007) Multiscale simulation of transmembrane proteins. J Struct Biol 157(3):570–578CrossRefGoogle Scholar
  10. 10.
    Gurtovenko AA, Anwar J, Vattulainen I (2010) Defect-mediated trafficking across cell membranes: insights from in silico modeling. Chem Rev 110(10):6077–6103. doi:10.1021/cr1000783 CrossRefGoogle Scholar
  11. 11.
    Izvekov S, Voth GA (2006) Multiscale coarse-graining of mixed phospholipid/cholesterol bilayers. J Chem Theory Comput 2(3):637–648. doi:10.1021/ct050300c CrossRefGoogle Scholar
  12. 12.
    Shi Q, Voth GA (2005) Multi-scale modeling of phase separation in mixed lipid bilayers. Biophys J 89(4):2385–2394CrossRefGoogle Scholar
  13. 13.
    Tepper HL, Voth GA (2006) Mechanisms of passive ion permeation through lipid bilayers: insights from simulations. J Phys Chem B 110(42):21327–21337. doi:10.1021/jp064192h CrossRefGoogle Scholar
  14. 14.
    Venturoli M, Sperotto MM, Kranenburg M, Smit B (2006) Mesoscopic models of biological membranes. Phys Rep Rev Sect Phys Lett 437(1–2):1–54. doi:10.1016/j.physrep.2006.07.006 Google Scholar
  15. 15.
    Marrink SJ, de Vries AH, Tieleman DP (2009) Lipids on the move: simulations of membrane pores, domains, stalks and curves. Biochim Biophys Acta 1788(1):149–168. doi:10.1016/j.bbamem.2008.10.006 CrossRefGoogle Scholar
  16. 16.
    Psachoulia E, Marshall DP, Sansom MSP (2010) Molecular dynamics simulations of the dimerization of transmembrane alpha-helices. Acc Chem Res 43(3):388–396. doi:10.1021/ar900211k CrossRefGoogle Scholar
  17. 17.
    Lyubartsev AP, Rabinovich AL (2011) Recent development in computer simulations of lipid bilayers. Soft Matter 7(1):25–39. doi:10.1039/c0sm00457j CrossRefGoogle Scholar
  18. 18.
    Burkett SL, Mann S (1996) Spatial organization and patterning of gold nanoparticles on self-assembled biolipid tubular templates. Chem Commun 3:321–322CrossRefGoogle Scholar
  19. 19.
    Bhattacharya S, Srivastava A (2003) Synthesis and characterization of novel cationic lipid and cholesterol-coated gold nanoparticles and their interactions with dipalmitoylphosphatidylcholine membranes. Langmuir 19(10):4439–4447. doi:10.1021/la0269513 CrossRefGoogle Scholar
  20. 20.
    Wallace EJ, Sansom MSP (2009) Carbon nanotube self-assembly with lipids and detergent: a molecular dynamics study. Nanotechnology 20(4):045101. doi:10.1088/0957-4484/20/4/045101 CrossRefGoogle Scholar
  21. 21.
    Lian T, Ho RJY (2001) Trends and developments in liposome drug delivery systems. J Pharm Sci 90(6):667–680CrossRefGoogle Scholar
  22. 22.
    Bolinger PY, Stamou D, Vogel H (2004) Integrated nanoreactor systems: triggering the release and mixing of compounds inside single vesicles. J Am Chem Soc 126(28):8594–8595. doi:10.1021/ja049023u CrossRefGoogle Scholar
  23. 23.
    Jang J, Yoon H (2005) Formation mechanism of conducting polypyrrole nanotubes in reverse micelle systems. Langmuir 21(24):11484–11489. doi:10.1021/la051447u CrossRefGoogle Scholar
  24. 24.
    Müller M, Katsov K, Schick M (2006) Biological and synthetic membranes: what can be learned from a coarse-grained description? Phys Rep 434(5–6):113–176CrossRefGoogle Scholar
  25. 25.
    Sintes T, Baumgaertner A (1998) Interaction of wedge-shaped proteins in flat bilayer membranes. J Phys Chem B 102(36):7050–7057CrossRefGoogle Scholar
  26. 26.
    Lenz O, Schmid F (2005) A simple computer model for liquid lipid bilayers. J Mol Liq 117(1–3):147–152. doi:10.1016/j.molliq.2004.08.008 CrossRefGoogle Scholar
  27. 27.
    Marrink SJ, de Vries AH, Mark AE (2003) Coarse grained model for semiquantitative lipid simulations. J Phys Chem B 108(2):750–760. doi:10.1021/jp036508g CrossRefGoogle Scholar
  28. 28.
    Marrink S-J, Mark AE (2004) Molecular view of hexagonal phase formation in phospholipid membranes. Biophys J 87(6):3894–3900CrossRefGoogle Scholar
  29. 29.
    Marrink SJ, Mark AE (2003) The mechanism of vesicle fusion as revealed by molecular dynamics simulations. J Am Chem Soc 125(37):11144–11145. doi:10.1021/ja036138+ CrossRefGoogle Scholar
  30. 30.
    Kawakatsu T (2004) Statistical physics of polymers. Springer, BerlinGoogle Scholar
  31. 31.
    Matsen MW, Schick M (1994) Stable and unstable phases of a diblock copolymer melt. Phys Rev Lett 72(16):2660–2663CrossRefGoogle Scholar
  32. 32.
    Drolet F, Fredrickson GH (1999) Combinatorial screening of complex block copolymer assembly with self-consistent field theory. Phys Rev Lett 83(21):4317–4320CrossRefGoogle Scholar
  33. 33.
    Fredrickson GH, Ganesan V, Drolet F (2002) Field-theoretic computer simulation methods for polymers and complex fluids. Macromolecules 35(1):16–39. doi:10.1021/ma011515t CrossRefGoogle Scholar
  34. 34.
    Lauw Y, Leermakers FAM, Stuart MAC (2006) Self-consistent-field analysis of the micellization of carboxy-modified poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) triblock copolymers. J Phys Chem B 110(1):465–477CrossRefGoogle Scholar
  35. 35.
    Ly DQ, Honda T, Kawakatsu T, Zvelindovsky AV (2008) Hexagonally perforated lamella-to-cylinder transition in a diblock copolymer thin film under an electric field. Macromolecules 41(12):4501–4505CrossRefGoogle Scholar
  36. 36.
    Dickinson E, Pinfield VJ, Home DS, Leermakers FAM (1997) Self-consistent-field modelling of adsorbed casein interaction between two protein-coated surfaces. J Chem Soc, Faraday Trans 93(9):1785–1790CrossRefGoogle Scholar
  37. 37.
    Balazs AC, Singh C, Zhulina E (1998) Modeling the interactions between polymers and clay surfaces through self-consistent field theory. Macromolecules 31(23):8370–8381CrossRefGoogle Scholar
  38. 38.
    Roan JR, Kawakatsu T (2002) Self-consistent-field theory for interacting polymeric assemblies. I. Formulation, implementation, and benchmark tests. J Chem Phys 116(16):7283–7294CrossRefGoogle Scholar
  39. 39.
    Roan JR, Kawakatsu T (2002) Self-consistent-field theory for interacting polymeric assemblies. II. Steric stabilization of colloidal particles. J Chem Phys 116(16):7295–7310CrossRefGoogle Scholar
  40. 40.
    Marcelja S (1973) Molecular model for phase transition in biological membranes. Nature 241(5390):451–453CrossRefGoogle Scholar
  41. 41.
    Leermakers FAM, Rabinovich AL, Balabaev NK (2003) Self-consistent-field modeling of hydrated unsaturated lipid bilayers in the liquid-crystal phase and comparison to molecular dynamics simulations. Phys Rev E 67(1):011910CrossRefGoogle Scholar
  42. 42.
    Leermakers FAM, Scheutjens J (1988) Statistical thermodynamics of association colloids. 1. Lipid bilayer-membranes. J Chem Phys 89(5):3264–3274CrossRefGoogle Scholar
  43. 43.
    Ayton G, McWhirter JL, Voth GA (2006) A second generation mesoscopic lipid bilayer model: connections to field-theory descriptions of membranes and nonlocal hydrodynamics. J Chem Phys 124(6):12. doi:10.1063/1.2165194 CrossRefGoogle Scholar
  44. 44.
    Muller M, Smith GD (2005) Phase separation in binary mixtures containing polymers: a quantitative comparison of single-chain-in-mean-field simulations and computer simulations of the corresponding multichain systems. J Polym Sci, Part B: Polym Phys 43(8):934–958CrossRefGoogle Scholar
  45. 45.
    Daoulas KC, Muller M, Stoykovich MP, Park SM, Papakonstantopoulos YJ, de Pablo JJ, Nealey PF, Solak HH (2006) Fabrication of complex three-dimensional nanostructures from self-assembling block copolymer materials on two-dimensional chemically patterned templates with mismatched symmetry. Phys Rev Lett 96(3):036104CrossRefGoogle Scholar
  46. 46.
    Detcheverry FA, Kang HM, Daoulas KC, Muller M, Nealey PF, de Pablo JJ (2008) Monte Carlo simulations of a coarse grain model for block copolymers and nanocomposites. Macromolecules 41(13):4989–5001CrossRefGoogle Scholar
  47. 47.
    Detcheverry FA, Pike DQ, Nealey PF, Müller M, de Pablo J (2010) Simulations of theoretically informed coarse grain models of polymeric systems. Faraday Discuss 144:111–125CrossRefGoogle Scholar
  48. 48.
    Milano G, Kawakatsu T (2009) Hybrid particle-field molecular dynamics simulations for dense polymer systems. J Chem Phys 130(21):214106CrossRefGoogle Scholar
  49. 49.
    Milano G, Kawakatsu T (2010) Pressure calculation in hybrid particle-field simulations. J Chem Phys 133(21):214102. doi:10.1063/1.3506776 CrossRefGoogle Scholar
  50. 50.
    De Nicola A, Zhao Y, Kawakatsu T, Roccatano D, Milano G (2011) Hybrid particle-field coarse-grained models for biological phospholipids. J Chem Theory Comput 7(9):2947CrossRefGoogle Scholar
  51. 51.
    Schmid F (1998) Self-consistent-field theories for complex fluids. J Phys: Condens Matter 10(37):8105–8138. doi:10.1088/0953-8984/10/37/002 CrossRefGoogle Scholar
  52. 52.
    Matsen MW (2002) The standard Gaussian model for block copolymer melts. J Phys Condens Matter 14(2):R21. doi:10.1088/0953-8984/14/2/201 CrossRefGoogle Scholar
  53. 53.
    Fredrickson GH (2005) The equilibrium theory of inhomogeneous polymers, vol 1. Oxford University Press, OxfordCrossRefGoogle Scholar
  54. 54.
    Helfand E, Tagami J (1972) Theory of the interface between immiscible polymers. II. J Chem Phys 56(7):10. doi:10.1063/1.1677735 CrossRefGoogle Scholar
  55. 55.
    Eastwood JW, Hockney RW, Lawrence DN (1980) P3M3DP—the three-dimensional periodic particle–particle/particle-mesh program. Comput Phys Commun 19(2):215CrossRefGoogle Scholar
  56. 56.
    Deserno M, Holm C (1998) How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines. J Chem Phys 109(12):7678CrossRefGoogle Scholar
  57. 57.
    Norizoe Y, Daoulas KC, Muller M (2010) Measuring excess free energies of self-assembled membrane structures. Faraday Discuss 144:369–391Google Scholar
  58. 58.
    Daoulas KC, Muller M (2006) Single chain in mean field simulations: Quasi-instantaneous field approximation and quantitative comparison with Monte Carlo simulations. J Chem Phys 125(18):184904CrossRefGoogle Scholar
  59. 59.
    Marrink S-J, Risselada HJ, Yefimov S, Tieleman DP, de Vries AH (2007) The MARTINI force field: coarse grained model for biomolecular simulations. J Phys Chem B 111(27):7812–7824. doi:10.1021/jp071097f CrossRefGoogle Scholar
  60. 60.
    Van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJC (2005) GROMACS: fast, flexible, and free. J Comput Chem 26(16):1701–1718CrossRefGoogle Scholar
  61. 61.
    Zhao Y, De Nicola A, Kawakatsu T, Milano G (2012) Hybrid particle-field molecular dynamics simulations: parallelization and benchmarks. J Comput Chem 33:868–880. doi:10.1002/jcc.22883 Google Scholar
  62. 62.
    Carbone P, Varzaneh HAK, Chen X, Muller-Plathe F (2008) Transferability of coarse-grained force fields: the polymer case. J Chem Phys 128(6):064904–064911CrossRefGoogle Scholar
  63. 63.
    Tuckerman ME, Glenn JM, Bruce JB (1990) Molecular dynamics algorithm for condensed systems with multiple time scales. J Chem Phys 93(2):5. doi:10.1063/1.459140 CrossRefGoogle Scholar
  64. 64.
    Moroi Y (1992) Micelles. Theoretical and applied aspects. Springer, BerlinGoogle Scholar

Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Antonio De Nicola
    • 1
    • 2
  • Ying Zhao
    • 1
  • Toshihiro Kawakatsu
    • 3
  • Danilo Roccatano
    • 4
  • Giuseppe Milano
    • 1
    • 2
  1. 1.Dipartimento di Chimica e BiologiaUniversità di SalernoFiscianoItaly
  2. 2.IMAST Scarl-Technological District in Polymer and Composite EngineeringPorticiItaly
  3. 3.Department of PhysicsTohoku UniversitySendaiJapan
  4. 4.Jacobs University BremenBremenGermany

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