Skip to main content
SpringerLink
Log in

Implicit solvent simulation models for biomembranes

  • Review
  • Published:
European Biophysics Journal Aims and scope Submit manuscript

Abstract

Fully atomic simulation strategies are infeasible for the study of many processes of interest to membrane biology, biophysics and biochemistry. We review various coarse-grained simulation methodologies with special emphasis on methods and models that do not require the explicit simulation of water. Examples from our own research demonstrate that such models have potential for simulating a variety of biologically relevant phenomena at the membrane surface.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10
Fig. 11
Fig. 12
Fig. 13
Fig. 14

Similar content being viewed by others

References

  • Allen MP (1993) Simulations using hard particles. Philos Trans Phys Sci Eng 344:323–337

    ADS  Google Scholar 

  • Aoki K, Yonezawa F (1992) Constant-pressure molecular-dynamics simulations of the crystal-smectic transition in systems of soft parallel spherocylinders. Phys Rev A 46:6541–6549

    ADS  Google Scholar 

  • Aranda-Espinoza H, Berman A, Dan N, Pincus P, Safran SA (1996) Interaction between inclusions embedded in membranes. Biophys J 71:648–656

    Google Scholar 

  • Ayton G, Voth GA (2002) Bridging microscopic and mesoscopic simulations of lipid bilayers. Biophys J 83:3357–3370

    Google Scholar 

  • Ayton G, Bardenhagen SG, McMurty P, Sulsky D, Voth GA (2001) Interfacing continuum and molecular dynamics: an application to lipid bilayers. J Chem Phys 114:6913–6924

    ADS  Google Scholar 

  • Bar-Ziv R, Menes R, Moses E, Safran SA (1995) Local unbinding of pinched membranes. Phys Rev Lett 75:3356–3359

    ADS  Google Scholar 

  • Ben-Shaul A (1995) Molecular theory of chain packing. In: Lipowsky R, Sackmann E (eds) Structure and dynamics of membranes, vol 1. Elsevier, Amsterdam

  • Bloom M, Evans E, Mouritsen OG (1991) Physical-properties of the fluid lipid-bilayer component of cell membranes—a perspective. Q Rev Biophys 24:293–397

    Google Scholar 

  • Boyd BJ, Drummond CJ, Krodkiewska I, Grieser F (2000) How chain length, headgroup polymerization, and anomeric configuration govern the thermotropic and lyotropic liquid crystalline phase behavior and the air–water interfacial adsorption of glucose-based surfactants. Langmuir 16:7359–7367

    Google Scholar 

  • Brannigan G, Brown FLH (2004) Solvent-free simulations of fluid membrane bilayers. J Chem Phys 120:1059

    ADS  Google Scholar 

  • Brannigan G, Brown FL (2005) Composition dependence of bilayer elasticity. J Chem Phys 122:074905

    ADS  Google Scholar 

  • Brannigan G, Tamboli AC, Brown FLH (2004) The role of molecular shape in bilayer phase behavior and elasticity. J Chem Phys 121:3259–3271

    ADS  Google Scholar 

  • Brannigan G, Philips PF, Brown FL (2005) Flexible lipid bilayers in implicit solvent. Phys Rev E 72:011915

    ADS  Google Scholar 

  • Brochard F, Lennon JF (1975) Frequency spectrum of the flicker phenomenon in erythrocytes. J Phys (Paris) 36:1035–1047

    Article  Google Scholar 

  • Brown FLH (2003) Regulation of protein mobility via thermal membrane undulations. Biophys J 84:842–853

    Google Scholar 

  • Brown FLH, Leitner DM, McCammon JA, Wilson KR (2000) Lateral diffusion of membrane proteins in the presence of static and dynamic corrals: suggestions for appropriate observables. Biophys J 78:2257–2269

    Article  Google Scholar 

  • Byers TJ, Branton D (1985) Visualization of the protein associations in the erythrocyte membrane skeleton. Proc Natl Acad Sci USA 82:6153–6157

    ADS  Google Scholar 

  • Canham PB (1970) The minimum energy of bending as a possible explanation of the biconcave shape of the red blood cell. J Theor Biol 26:61–81

    Google Scholar 

  • Chao C-Y, Chou C-F, Ho JT, Hui S, Jin A, Huang CC (1996) Nature of layer-by-layer freezing in free-standing 4o.8 films. Phys Rev Lett 77:2750–2753

    ADS  Google Scholar 

  • Cheng M, Ho JT, Hui SW, Pindak R (1988) Observation of two-dimensional hexatic behavior in free-standing liquid crystal films. Phys Rev Lett 61:550–553

    ADS  Google Scholar 

  • Cherry RJ (1979) Rotational and lateral diffusion of membrane proteins. Biochim Biophys Acta 559:289–327

    Google Scholar 

  • Chiu SW, Jakobsson E, Mashl RJ, Scott HL (2002) Cholesterol-induced modifications in lipid bilayers: a simulation study. Biophys J 83:1842–1853

    Google Scholar 

  • Chiu S, Vasudevan S, Jakobsson E, Mashl RJ, Scott HL (2003) Structure of sphingomyelin bilayers: a simulation study. Biophys J 85:3624–3635

    Google Scholar 

  • Chou C-F, Jin AJ, Hui S, Huang CC, Ho JT (1998) Multiple-step melting in two-dimensional hexatic liquid-crystal films. Science 280:1424–1426

    ADS  Google Scholar 

  • Cooke IR, Kremer K, Deserno M (2005) Tunable generic model for fluid bilayer membranes. Phys Rev E 72:011506

    Google Scholar 

  • Corbett JD, Agre P, Palek J, Golan DE (1994) Differential control of band 3 lateral and rotational mobility in intact red cells. J Clin Invest 94:683–688

    Article  Google Scholar 

  • Dan N, Pincus P, Safran SA (1993) Membrane-induced interactions between inclusions. Langmuir 9:2768–2771

    Google Scholar 

  • Dan N, Berman A, Pincus P, Safran SA (1994) Membrane-induced interactions between inclusions. J Phys II France 4:1713–1725

    Google Scholar 

  • Deuling HJ, Helfrich W (1976) The curvature elasticity of fluid membranes: a catalogue of vesicle shapes. J Phys (Paris) 37:1335–1345

    Google Scholar 

  • Dill KA, Bromberg S, Yue K, Fiebig KM, Yee DP, Thomas PD, Chan HS (1995) Principles of protein folding—a perspective from simple exact models. Protein Sci 4:561–602

    Google Scholar 

  • Doi M, Edwards SF (1986) The theory of polymer dynamics. Clarendon Press, Oxford

    Google Scholar 

  • Drouffe J-M, Maggs AC, Leibler S (1991) Computer simulations of self-assembled membranes. Science 254:1353–1356

    ADS  Google Scholar 

  • Edidin M, Kuo SC, Sheetz MP (1991) Lateral movements of membrane glycoproteins restricted by dynamic cytoplasmic barriers. Science 254:1379–1382

    ADS  Google Scholar 

  • Edwards L, Peng Y, Reggia JA (1998) Computational models for the formation of protocell structures. Artif Life 4:61–77

    Google Scholar 

  • Ermak DL, McCammon JA (1978) Brownian dynamics with hydrodynamic interactions. J Chem Phys 69:1352–1360

    ADS  Google Scholar 

  • Evans E (1974) Bending resistance and chemically induced moments in membrane bilayers. Biophys J 14:923–931

    Article  Google Scholar 

  • Evans E, Skalak R (1980) Mechanisms and thermodyanmics of biomembranes. CRC Press, Boca Raton

    Google Scholar 

  • Farago O (2003) “Water-free” computer model for fluid bilayer membranes. J Chem Phys 119:596–605

    ADS  Google Scholar 

  • Farago O (2004) Statistical mechanics of bilayer membrane with a fixed projected area. J Chem Phys 120:2934–2950

    ADS  Google Scholar 

  • Fattal D, Ben-Shaul A (1993) A molecular model for lipid–protein interaction in membranes: the role of hydrophobic mismatch. Biophys J 65:1795–1809

    Google Scholar 

  • Feig M, Brooks CL III (2004) Recent advances in the development and application of implicit solvent models in biomolecule simulations. Curr Opin Struct Biol 14:217–224

    Google Scholar 

  • Feller SE (2000) Molecular dynamics simulations of lipid bilayers. Curr Opin Colloid Interface 5:217–223

    Google Scholar 

  • Geer R, Stoebe T, Huang CC, Pindak R, Goodby J, Cheng M, Ho JT, Hui SW (1992) Liquid–hexatic phase transitions in single molecular layers of liquid-crystal films. Nature 355:152–154

    ADS  Google Scholar 

  • deGennes P, Prost J (1993) The physics of liquid crystals, 2nd edn. Clarendon Press, Oxford

    Google Scholar 

  • Gennis RB (1989) Biomembranes: molecular structure and function. Springer, Berlin Heidelberg New York

    Google Scholar 

  • Goetz R, Lipowsky R (1998) Computer simulations of bilayer membranes: self assembly and interfacial tension. J Chem Phys 108:7397–7409

    ADS  Google Scholar 

  • Goetz R, Gompper G, Lipowsky R (1999) Mobility and elasticity of self-assembled membranes. Phys Rev Lett 82:221–224

    ADS  Google Scholar 

  • Gompper G, Kroll DM (1997) Network models of fluid, hexatic and polymerized membranes. J Phys Condens Matter 9:8795–8834

    ADS  Google Scholar 

  • Gouliaev N, Nagle JF (1998a) Simulations of a single membrane between two walls using a Monte Carlo method. Phys Rev E 58:881–888

    ADS  Google Scholar 

  • Gouliaev N, Nagle JF (1998b) Simulations of interacting membranes in the soft confinement regime. Phys Rev Lett 81:2610–2613

    ADS  Google Scholar 

  • Gov N (2004) Membrane undulations driven by force fluctuations of active proteins. Phys Rev Lett 93:268104

    ADS  Google Scholar 

  • Gov N, Safran SA (2004) Pinning of fluid membranes by periodic harmonic potentials. Phys Rev E 69:011101

    ADS  MathSciNet  Google Scholar 

  • Gov N, Zilman AG, Safran S (2003) Cytoskeleton confinement and tension of red blood cells. Phys Rev Lett 90:228101

    ADS  Google Scholar 

  • Gov N, Zilman AG, Safran SA (2004) Hydrodynamics of confined membranes. Phys Rev E 70:011104

    ADS  MathSciNet  Google Scholar 

  • Gove PB (ed) (1970) Webster’s seventh new collegiate dictionary. G. & C. Merriam, Springfield

    Google Scholar 

  • Grakoui A, Bromley SK, Sumen C, Davis MM, Shaw AS, Allen PM, Dustin ML (1999) The immunological synapse: a molecular machine controlling t cell activation. Science 285:221–227

    Google Scholar 

  • Granek R (1997) From semi-flexible polymers to membranes: anomalous diffusion and reptation. J Phys II (Paris) 7:1761–1788

    Google Scholar 

  • Granek R, Klafter J (2001) Anomalous motion of membranes under a localized external potential. Europhys Lett 56:15–21

    ADS  Google Scholar 

  • Groot RD, Rabone KL (2001) Mesoscopic simulation of cell membrane damage, morphology change and rupture by nonionic surfactants. Biophys J 81:725

    Google Scholar 

  • Gruhn T, Lipowsky R (2005) Temperature dependence of vesicle adhesion. Phys Rev E 71:011903

    ADS  Google Scholar 

  • Harries D, Ben-Shaul A (1997) Conformational chain statistics in a model lipid bilayer: comparison between mean field and Monte Carlo calculations. J Chem Phys 106:1609–1619

    ADS  Google Scholar 

  • Harroun TA, Heller WT, Weiss T, Yang L, Huang HW (1999) Experimental evidence for hydrophobic matching and membrane-mediated interactions in lipid bilayers containing gramicidin. Biophys J 76:937–945

    Google Scholar 

  • Helfrich W (1973) Elastic properties of lipid bilayers: theory and possible experiments. Z Naturforsch 28c:693–703

    Google Scholar 

  • Helfrich W (1978) Steric interaction of fluid membranes in multilayer systems. Z Naturforsch 33a:305–315

    ADS  Google Scholar 

  • Helfrich P, Jakobsson E (1990) Calculation of deformation energies and conformations in lipid membranes containing gramicidin channels. Biophys J 57:1075–1084

    Article  Google Scholar 

  • Holzöhner R, Schoen M (1999) Attractive forces between anisotropic inclusions in the membrane of a vesicle. Eur Phys J B 12:413–419

    ADS  Google Scholar 

  • Huang H (1986) Deformation free energy of bilayer membrane and its effects on gramicidin channel lifetime. Biophys J 50:1061–1070

    Google Scholar 

  • Illya G, Lipowsky R, Shillcock JC (2005) Effect of chain length and asymmetry on material properties of bilayer membranes. J Chem Phys 122:244901

    ADS  Google Scholar 

  • Im W, Feig M, Brooks CL III (2003) An implicit membrane generalized born theory for the study of structure, stability and interactions of membrane proteins. Biophys J 85:2900–2918

    Google Scholar 

  • Imparato A, Shillcock J, Lipowsky R (2005) Shape fluctuations and elastic properties of two-component bilayer membranes. Europhys Lett 69:650–656

    ADS  Google Scholar 

  • Izvekov S, Voth GA (2005) A multi-scale coarse-graining method for biomolecular systems. J Phys Chem B 109:2469

    Google Scholar 

  • Jamney P (1995) Cell membranes and the cytoskeleton. In: Structure and dynamics of membranes: part A. From cells to vesicles. Elsevier, Amsterdam, pp 805–849

  • Jensen MO, Mouritsen OG (2004) Lipids do influence protein function—the hydrophobic matching hypothesis revisited. Biochim Biophys Acta 1666:205–226

    Google Scholar 

  • Kaizuka Y, Groves JT (2004) Structure and dynamics of supported intermembrane junctions. Biophys J 86:905–912

    Article  Google Scholar 

  • van Kampen NG (1992) Stochastic processes in physics and chemistry. North-Holland, Amsterdam, pp 63, 83, 220-221

  • Kohyama T, Kroll D, Gompper G (2003) Budding of crystalline domains in fluid membranes. Phys Rev E 68:061905

    ADS  Google Scholar 

  • Kolinski A, Skolnick J (2004) Reduced models of proteins and their applications. Polymer 45:511–524

    Google Scholar 

  • Koppel DE, Sheetz MP, Schindler M (1981) Matrix control of protein diffusion in biological membranes. Proc Natl Acad Sci USA 78:3576–3580

    ADS  Google Scholar 

  • Kralchevsky P, Paunov V, Dekov ND, Nagayama K (1991) Stresses in lipid membranes and interactions between inclusions. J Chem Soc Faraday Trans 91:3415–3432

    Google Scholar 

  • Kumar PS, Rao M (1998) Shape instabilities in the dynamics of a two-component fluid membrane. Phys Rev Lett 80:2489–2492

    ADS  Google Scholar 

  • Kumar PS, Gompper G, Lipowsky R (2001) Budding dynamics of multicomponent membranes. Phys Rev Lett 86:3911–3914

    ADS  Google Scholar 

  • Kusumi A, Sako Y (1996) Cell surface organization by the membrane skeleton. Curr Opin Cell Biol 8:566–574

    Google Scholar 

  • Kusumi A, Sako Y, Yamamoto M (1993) Confined lateral diffusion of membrane receptors as studied by single particle tracking. Effects of calcium-induced differentiation in cultured epithelial cells. Biophys J 65:2021–2040

    Google Scholar 

  • Lambacher A, Fromhertz P (1996) Fluorescence interference-contrast microscopy on oxidized silicon using a monomolecular dye layer. Appl Phys A 63:207–216

    ADS  Google Scholar 

  • Laradji M (1999) Polymer adsorption on fluctuating surfaces. Europhys Lett 47:694–700

    ADS  Google Scholar 

  • Laradji M (2002) Elasticity of polymer-anchored membranes. Europhys Lett 60:594–600

    ADS  Google Scholar 

  • Laradji M (2004) A Monte Carlo study of fluctuating polymer-grafted membranes. J Chem Phys 121:1591–1600

    ADS  Google Scholar 

  • Laradji M, Kumar PS (2004) Dynamics of domain growth in self-assembled fluid vesicles. Phys Rev Lett 93:198105

    ADS  Google Scholar 

  • Leitner DM, Brown FLH, Wilson KR (2000) Regulation of protein mobility in cell membranes: a dynamic corral model. Biophys J 78:125–135

    Google Scholar 

  • Lim HWG, Wortis M, Mukhopadhyay R (2002) Stomatocyte–discocyte–echinocyte sequence of the human red blood cell: evidence for the bilayer-couple hypothesis from membrane mechanics. Proc Natl Acad Sci 99:16766–16769

    ADS  Google Scholar 

  • Lin LC-L, Brown FLH (2004a) Brownian dynamics in fourier space: membrane simulations over long length and time scales. Phys Rev Lett 93:256001

    ADS  Google Scholar 

  • Lin LC-L, Brown FLH (2004b) Dynamics of pinned membranes with application to protein diffusion on the surface of red blood cells. Biophys J 86:764–780

    Google Scholar 

  • Lin LC-L, Brown FLH (2005) Dynamic simulations of membranes with cytoskeletal interactions. Phys Rev E 72:011910

    ADS  Google Scholar 

  • Lindahl E, Edholm O (2000a) Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations. Biophys J 79:426–633

    Google Scholar 

  • Lindahl E, Edholm O (2000b) Spatial and energetic-entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations. J Chem Phys 113:3882–3893

    ADS  Google Scholar 

  • Lipowsky R (1991) The conformation of membranes. Nature 349:475–481

    ADS  Google Scholar 

  • Lipowsky R, Grotehans S (1994) Renormalization of hydration forces by collective protrusion modes. Biophys Chem 49:27–37

    Google Scholar 

  • Lipowsky R, Sackmann E (1995) Structure and dynamics of membranes. Elsevier, Amsterdam

    MATH  Google Scholar 

  • Lipowsky R, Zielenska B (1989) Binding and unbinding of lipid membranes: a Monte Carlo study. Phys Rev Lett 62:1572–1575

    ADS  Google Scholar 

  • Liu S, Derick L, Palek J (1987) Visualization of the hexagonal lattice in the erythrocyte membrane skeleton. J Cell Biol 104:527–536

    Google Scholar 

  • Lodish H, Baltimore D, Berk A, Zipursky SL, Matsudaira P, Darnell J (1995) Molecular cell biology, 3rd edn. Scientific American Books, New York

    Google Scholar 

  • Loison C, Mareschal M, Kremer K, Schmid F (2003) Thermal fluctuations in a lamellar phase of a binary amphiphile–solvent mixture: a molecular-dynamics study. J Chem Phys 119:13138–13148

    ADS  Google Scholar 

  • Luna EJ, Hitt AL (1992) Cytoskeleton–plasma membrane interactions. Science 258:955–964

    ADS  Google Scholar 

  • Luzzati V (1968) X-ray diffraction studies of lipid-water systems. In: Chapman D (ed) Biological membranes, vol 1. Academic, New York, pp 71–123

  • Luzzati V, Husson F (1962) Structure of liquid-crystalline phases of lipid water systems. J Cell Biol 12:207

    Google Scholar 

  • Manneville J-B, Bassereau P, Levy D, Prost J (1999) Activity of transmembrane proteins induces magnification of shape fluctuations of lipid membranes. Phys Rev Lett 82:4356–4359

    ADS  Google Scholar 

  • Manneville J-B, Bassereau P, Ramaswamy S, Prost J (2001) Active membrane fluctuations studied by micropipet aspiration. Phys Rev E 64:021908

    ADS  Google Scholar 

  • Marčelja S (1976) Lipid-mediated protein interaction in membranes. Biochim Biophys Acta 455:1–7

    Google Scholar 

  • Marrink SJ, Mark AE (2001) Effect of undulations on surface tension in simulated bilayers. J Phys Chem 105:6122–6127

    Google Scholar 

  • Marrink S-J, Berkowitz M, Berendsen HJC (1993) Molecular dynamics simulation of a membrane/water interface: the ordering of water and its relation to the hydration force. Langmuir 9:3122–3131

    Google Scholar 

  • Marrink S-J, Lindahl E, Edholm O, Mark AE (2001) Simulation of the spontaneous aggregation of phospholipids into bilayers. J Am Chem Soc 2001:8638–8639

    Google Scholar 

  • Marrink S, de Vries A, Mark AE (2004) Coarse grained model for semiquantitative lipid simulations. J Phys Chem B 108:750–760

    Google Scholar 

  • May S (2000) Theories on structural perturbations of lipid bilayers. Curr Opin Colloid Interface Sci 5:244–249

    Google Scholar 

  • McWhirter JL, Ayton G, Voth GA (2004) Coupling field theory with mesoscopic dynamical simulations of multicomponent lipid bilayers. Biophys J 87:3242–3263

    Google Scholar 

  • Miao L, Fourcade B, Wortis MRM, Zia RKP (1991) Equilibrium budding and vesiculation in the curvature model of fluid lipid vesicles. Phys Rev A 43:6843–6856

    ADS  Google Scholar 

  • Miao L, Seifert U, Wortis M, Döbereiner H (1994) Budding transitions of fluid-bilayer vesicles: the effect of area-difference elasticity. Phys Rev E 49:5389–5407

    ADS  Google Scholar 

  • Milner ST, Safran SA (1987) Dynamical fluctuations of droplet microemulsions and vesicles. Phys Rev A 36:4371–4379

    ADS  Google Scholar 

  • Moore GE (1985) Cramming more components onto integrated circuits. Electronics 38:114–117

    Google Scholar 

  • Morikawa R, Saito Y (1994) Hard rod and frustum model of two-dimensional vesicles. J Phys II 4:145

    Google Scholar 

  • Mukhopadhyay R, Lim HWG, Wortis M (2002) Echinocyte shapes: bending, stretching, and shear determine spicule shape and spacing. Biophys J 82:1756–1772

    Google Scholar 

  • Murtola T, Falck E, Patra M, Karttunen M, Vattulainen I (2004) Coarse-grained model for phospholipid/cholesterol bilayer. J Chem Phys 121:9156–9165

    ADS  Google Scholar 

  • Nagle JF, Tristram-Nagle S (2000) Structure of lipid bilayers. Biochim Biophys Acta 1469:159–195

    Google Scholar 

  • Netz RR (1997) Inclusions in fluctuating membranes: exact results. J Phys I France 7:833–852

    Google Scholar 

  • Nielsen C, Goulian M, Andersen OS (1998) Energetics of inclusion-induced bilayer deformations. Biophys J 74:1966–1983

    Google Scholar 

  • Nielsen SO, Ensing B, Ortiz V, Moore PB, Klein ML (2005) Lipid bilayer perturbations around a transmembrane nanotube: a coarse grain molecular dynamics study. Biophys J 88:3822–3828

    Google Scholar 

  • Noguchi H (2002) Fusion and toroidal formation of vesicles by mechanical forces: a brownian dynamics simulation. J Chem Phys 117:8130–8137

    ADS  Google Scholar 

  • Noguchi H (2003) Polyhedral vesicles: a brownian dynamics simulation. Phys Rev E 67:041901

    ADS  Google Scholar 

  • Noguchi H, Gompper G (2004) Fluid vesicles with viscous membranes in shear flow. Phys Rev Lett 93:258102

    ADS  Google Scholar 

  • Noguchi H, Takasu M (2001a) Fusion pathways of vesicles: a brownian dynamics simulation. J Chem Phys 115:9547–9551

    ADS  Google Scholar 

  • Noguchi H, Takasu M (2001b) Self-assembly of amphiphiles into vesicles: a brownian dynamics simulation. Phys Rev E 64:041913

    ADS  Google Scholar 

  • Noguchi H, Takasu M (2002a) Adhesion of nanoparticles to vesicles: a brownian dynamics simulation. Biophys J 83:299–308

    Article  Google Scholar 

  • Noguchi H, Takasu M (2002b) Structural changes of pulled vesicles: a brownian dynamics simulation. Phys Rev E 65:051907

    ADS  Google Scholar 

  • Owicki J, McConnell HM (1979) Theory of protein–lipid and protein–protein interactions in bilayer membranes. Proc Natl Acad Sci 76:4750–4754

    ADS  Google Scholar 

  • Partenskii MB, Jordan PC (2002) Membrane deformation and the elastic energy of insertion: perturbation of membrane elastic constants to due peptide insertion. J Chem Phys 117:10768–10776

    ADS  Google Scholar 

  • Parthasarathy R, Groves JT (2004) Optical techniques for imaging membrane topography. Cell Biochem Biophys 41:391–414

    Google Scholar 

  • Pastor RW (1994) Molecular-dynamics and Monte-Carlo simulations of lipid bilayers. Curr Opin Struct Biol 4:486–492

    Google Scholar 

  • Petrache H, Zuckerman D, Sachs J, Killian J, Koeppe R, Woolf TB (2002) Hydrophobic matching mechanism investigated by molecular dynamics simulations. Langmuir 18:1340–1351

    Google Scholar 

  • Pindak R, Moncton DE, Davey SC, Goodby JW (1981) X-ray observation of a stacked hexatic liquid-crystal b phase. Phys Rev Lett 46:1135

    ADS  Google Scholar 

  • Pitman MC, Grossfield A, Suits F, Feller SE (2005) Role of cholesterol and polyunsaturated chains in lipid–protein interactions: molecular dynamics simulation of rhodopsin in a realistic membrane environment. J Am Chem Soc 127:4576–4577

    Google Scholar 

  • de Planque M, Killian J (2003) Protein–lipid interactions studied with designed transmembrane peptides: role of hydrophobic matching and interfacial anchoring. Mol Membr Biol 20:271–284

    Google Scholar 

  • Planque MRD, Greathouse D, Koeppe R, Schäfer H, Marsh D, Killian JA (1998) Influence of lipid/peptide hydrophobic mismatch on the thickness of diacylphosphatidylcholine bilayers: a 2H-nmr and esr study using designed transmembrane α-helical peptides and gramicidin a. Biochemistry 37:9333–9345

    Google Scholar 

  • Prost J, Bruinsma R (1996) Shape fluctuations of active membranes. Europhys Lett 33:321–326

    ADS  Google Scholar 

  • Prost J, Manneville J-B, Bruinsma R (1998) Fluctuation-magnification of non-equilibrium membranes near a wall. Eur Phys J B 1:465–480

    ADS  Google Scholar 

  • Purcell EM (1977) Life at low reynolds number. Am J Phys 45:3–10

    ADS  Google Scholar 

  • Qi SY, Groves JT, Chakraborty AK (2001) Synaptic pattern formation during cellular recognition. Proc Natl Acad Sci USA 98:6548–6553

    ADS  Google Scholar 

  • Ramaswamy S, Toner J, Prost J (1999) Nonequilibrium noise and instabilities in membranes with active pumps. Pramana J Phys 53:237–242

    ADS  Google Scholar 

  • Ramaswamy S, Toner J, Prost J (2000) Nonequilibrium fluctuations, traveling waves, and instabilities in active membranes. Phys Rev Lett 84:3494–3497

    ADS  Google Scholar 

  • Rand RP, Parsegian VA (1989) Hydration forces between phospholipid-bilayers. Biochim Biophys Acta 988:351–376

    Google Scholar 

  • Rawicz W, Oldbrich K, McIntosh T, Needham D, Evans E (2000) Effect of chain length and unsaturation on elasticity of lipid bilayers. Biophys J 79:328–339

    Google Scholar 

  • Rekvig L, Kranenburg M, Vreede J, Hafskjold B, Smit B (2003) Investigation of surfactant efficiency using dissipative particle dynamics. Langmuir 19:4897

    Google Scholar 

  • Sackmann E (1995a) Biological membranes architecture and function. In: Structure and dynamics of membranes: part A. From cells to vesicles. Elsevier, Amsterdam, pp 1–62

  • Sackmann E (1995b) Physical basis of self-organization and function of membranes: physics of vesicles. In: Lipowsky R, Sackmann E (eds) Structure and dynamics of membranes, vol 1. Elsevier, Amsterdam

  • Sackmann E (1996) Supported membranes: scientific and practical applications. Science 271:43–48

    ADS  Google Scholar 

  • Sackmann E, Tanaka M (2000) Supported membranes on soft polymer cushions: fabrication, characterization, and applications. Trends Biotechnol 18:58–64

    Google Scholar 

  • Saffman PG, Delbruck M (1975) Brownian motion in biological membranes. Proc Natl Acad Sci USA 73:3111–3113

    ADS  Google Scholar 

  • Safinya CR, Sirota EB, Roux D, Smith GS (1989) Universality in interacting membranes: the effect of cosurfactants on the interfacial rigidity. Phys Rev Lett 62:1134–1137

    ADS  Google Scholar 

  • Safran SA (1983) Fluctuations of spherical microemulsions. J Chem Phys 78:2073–2076

    ADS  Google Scholar 

  • Safran SA (1994) Statistical thermodynamics of surfaces, interfaces and membranes. Westview Press, Boulder

    Google Scholar 

  • Saxton MJ (1989) The spectrin network as a barrier to lateral diffusion in erythrocytes: a percolation analysis. Biophys J 55:21–28

    Article  Google Scholar 

  • Saxton MJ (1990a) The membrane skeleton of erythrocytes: a percolation model. Biophys J 57:1167–1177

    Google Scholar 

  • Saxton MJ (1990b) The membrane skeleton of erythrocytes: models of its effect on lateral diffusion. Int J Biochem 22:801–809

    Google Scholar 

  • Saxton MJ (1995) Single-particle tracking: effects of corrals. Biophys J 69:389–398

    ADS  Google Scholar 

  • Schindler M, Koppel DE, Sheetz MP (1980) Modulation of protein lateral mobility by polyphosphates and polyamines. Proc Natl Acad Sci USA 77:1457–1461

    ADS  Google Scholar 

  • Schneider M, Jenkins J, Webb W (1984) Thermal fluctuations of large quasi-spherical bimolecular phospholipid-vesicles. J Phys (Paris) 45:1457

    Google Scholar 

  • Seifert U (1994) Dynamics of a bound membrane. Phys Rev E 49:3124–3127

    ADS  Google Scholar 

  • Seifert U, Lipowsky R (1995) Morphology of vesicles. In: Lipowsky R, Sackmann E (eds) Structure and dynamics of membranes, vol 1. Elsevier, Amsterdam

  • Seifert U, Berndl K, Lipowsky R (1991) Shape transformations of vesicles: phase diagram for spontaneous-curvature and bilayer-coupling models. Phys Rev A 44:1182–1202

    ADS  Google Scholar 

  • Sheetz MP (1983) Membrane skeletal dynamics: role in modulation of red blood deformability, mobility of transmembrane proteins and shape. Sem Hematol 20:175–188

    Google Scholar 

  • Sheetz MP, Schindler M, Koppel DE (1980) The lateral mobility of integral membrane proteins is increased in spherocytic erythrocytes. Nature 285:510–512

    ADS  Google Scholar 

  • Shelley JC, Shelley MY (2000) Computer simulation of surfactant solutions. Curr Opin Colloid Interface Sci 5:101–110

    Google Scholar 

  • Shelley JC, Shelley MY, Reeder RC, Bandyopadhyay S, Klein ML (2001) A coarse grain model for phospholipid simulations. J Phys Chem B 105:4464–4470

    Google Scholar 

  • Shillcock J, Lipowsky R (2002) Equilibrium structure and lateral stress distribution of amphiphilic bilayers from dissipative particle dynamics. J Chem Phys 117:5048–5061

    ADS  Google Scholar 

  • Singer SJ, Nicolson GL (1972) The fluid mosaic model of the structure of cell membranes. Science 175:720–731

    ADS  Google Scholar 

  • Sintes T, Baumgärtner A (1998a) Interaction of wedge-shaped proteins in flat bilayer membranes. J Phys Chem B 1998:7050–7057

    Google Scholar 

  • Sintes T, Baumgärtner A (1998b) Membrane-mediated protein attraction. a Monte-Carlo study. Physica A 249:571–575

    Google Scholar 

  • Smit B, Hilbers P, Esselink K, Rupert L, van Os N, Schlijper AG (1991) Structure of a water oil interface in the presence of micelles—a computer simulation study. J Phys Chem 95:6361

    Google Scholar 

  • Smith G, Sirota E, Safinya C, Clark N (1988) Structure of the l β phases in a hydrated phosphatidylcholine multimembrane. Phys Rev Lett 60:813–816

    ADS  Google Scholar 

  • Smith G, Sirota E, Safinya C, Plano R, Clark N (1990) X-ray structural studies of freely suspended ordered hydrated dmpc multimembrane films. J Chem Phys 92:4519–4529

    ADS  Google Scholar 

  • Smondyrev AM, Berkowitz ML (1999) Structure of dipalmitoylphosphatidylcholine/cholesterol bilayer at low and high cholesterol concentrations: molecular dynamics simulation. Biophys J 77:2075–2089

    Google Scholar 

  • Soddemann T, Dunweg B, Kremer K (2001) A generic computer model for amphiphilic systems. Eur Phys J E 6:409–419

    Google Scholar 

  • Stadler C, Schmid F (1999) Phase behavior of grafted chain molecules: influence of head size and chain length. J Chem Phys 110:9697

    ADS  Google Scholar 

  • Steck TL (1989) Red cell shape. In: Stein W, Bronner F (eds) Cell shape: determinants, regulation and regulatory role. Academic, New York, pp 205–246

    Google Scholar 

  • Stevens MJ (2004) Coarse-grained simulations of lipid bilayers. J Chem Phys 121:11942

    ADS  Google Scholar 

  • Tien HT, Ottova-Leitmannova A (2003) Planar lipid bilayers (BLMs) and their applications. Elsevier, Amsterdam

    Google Scholar 

  • Tobias DJ, Tu KC, Klein ML (1997) Atomic-scale molecular dynamics simulations of lipid membranes. Curr Opin Colloid Interface 2:15–26

    Article  Google Scholar 

  • Tomishige M, Sako Y, Kusumi A (1998) Regulation mechanism of the lateral diffusion of band 3 in erythrocyte membranes by the membrane skeleton. J Cell Biol 142:989–1000

    Google Scholar 

  • Tsuji A, Ohnishi S (1986) Restriction of the lateral motion of band 3 in the erythrocyte membrane by the cytoskeletal network: dependence on spectrin association state. Biochemistry 25:6133–6139

    Google Scholar 

  • Tsuji A, Kawasaki K, Ohnishi S, Merkle H, Kusumi A (1988) Regulation of band 3 mobilities in erythrocyte ghost membranes by protein association and cytoskeletal meshwork. Biochemistry 27:7447–7452

    Google Scholar 

  • Venturoli M, Smit B, Sperotto MM (2005) Simulation studies of protein-induced bilayer deformations, and lipid-induced protein tilting, on a mesoscopic model for lipid bilayers with embedded proteins. Biophys J 88:1778–1798

    Google Scholar 

  • Wang Z, Frenkel D (2005) Modeling flexible amphiphilic bilayers: a solvent-free off-lattice Monte Carlo study. J Chem Phys 135:234711

    ADS  Google Scholar 

  • Weikl TR, Lipowsky R (2000) Local adhesion of membranes to striped surface domains. Langmuir 16:9338–9346

    Google Scholar 

  • Weis J, Levesque D, Zarragoicoechea G (1992) Orientational order in simple dipolar liquid-crystal models. Phys Rev Lett 69:913–916

    ADS  Google Scholar 

  • Weiss TM, van der Wel PC, Killian JA, Koeppe RE, Huang HW (2003) Hydrophobic mismatch between helices and lipid bilayers. Biophys J 84:379–385

    Article  Google Scholar 

  • Whitehead L, Edge CM, Essex JW (2001) Molecular dynamics simulation of the hydrocarbon region of a biomembrane using a reduced representation model. J Comput Chem 22:1622–1633

    Google Scholar 

  • Yamamoto S, Maruyama Y, Hyodo S-A (2002) Dissipative particle dynamics study of spontaneous vesicle formation of amphiphilic molecules. J Chem Phys 116:5842–5849

    ADS  Google Scholar 

  • Zangi R, Rice SA (2003) Freezing transition and correlated motion in a quasi-two-dimensional colloid suspension. Phys Rev E 68:061508

    ADS  Google Scholar 

  • Zeman K, Engelhard H, Sackmann E (1990) Bending undulations and elasticity of the erythrocyte membrane: effects of cell shape and membrane organization. Eur Biophys J 18:203–219

    Google Scholar 

  • Zhang D, Klyatkin A, Bolin JT, Low PS (2000) Crystallographic structure and functional interpretation of the cytoplasmic domain of erythrocyte membrane band 3. Blood 96:2925–2933

    Google Scholar 

  • Zilker A, Engelhardt H, Sackmann E (1987) Dynamic reflection interference contrast (ric-) microscopy: a new method to study surface excitations of cells and to measure membrane bending elastic moduli. J Phys (Paris) 48:2139–2151

    Google Scholar 

  • Zilker A, Engelhardt H, Sackmann E (1992) Spectral analysis of erythrocyte flickering in the 0.3–4 μm−1 regime by microinterferometry combined with fast image processing. Phys Rev A 46:7998–8001

    ADS  Google Scholar 

  • Zilman AG, Granek R (1996) Undulations and dynamic structure factor of membranes. Phys Rev Lett 77:4788–4791

    ADS  Google Scholar 

Download references

Acknowledgments

This work was supported in part by the NSF (MCB-0203221, CHE-0349196, CHE-0321368) and the donors of the American Chemical Society Petroleum Research Fund (PRF 42447-G7). F. B. is an Alfred P. Sloan Research Fellow. F. B. thanks the NSF for travel funds to participate in the “Biophysical Chemistry Meets Molecular Medicine” workshop.

Author information

Authors and Affiliations

  1. Department of Physics and Astronomy, University of California, Santa Barbara, CA, 93106-9530, USA

    Grace Brannigan & Lawrence C.-L. Lin

  2. Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106-9510, USA

    Frank L. H. Brown

Authors
  1. Grace Brannigan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Lawrence C.-L. Lin
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Frank L. H. Brown
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Frank L. H. Brown.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Brannigan, G., Lin, L.CL. & Brown, F.L.H. Implicit solvent simulation models for biomembranes. Eur Biophys J 35, 104–124 (2006). https://doi.org/10.1007/s00249-005-0013-y

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00249-005-0013-y

Keywords

Search

Navigation